[](https://gitpod.io/#https://github.com/bactopia/bactopia-py)
# bactopia-py
A Python package for working with [Bactopia](https://bactopia.github.io/)
## Bactopia Subcommands
There are many subcommands available in Bactopia. Here is a brief description of each command:
| Command | Description |
|---------------------------|----------------------------------------------------------------------------|
| `bactopia-citations` | Print out tools and citations used throughout Bactopia |
| `bactopia-datasets` | Download optional datasets to supplement your analyses with Bactopia |
| `bactopia-download` | Builds Bactopia environments for use with Nextflow. |
| `bactopia-prepare` | Create a 'file of filenames' (FOFN) of samples to be processed by Bactopia |
| `bactopia-search` | Query against ENA and SRA for public accessions to process with Bactopia |
| `bactopia-summary` | Generate a summary table from the Bactopia results. |
| `bactopia-atb-downloader` | Download assemblies from AllTheBacteria for use with Bactopia Tools |
| `bactopia-atb-formatter` | Restructure All-the-Bacteria assemblies to allow usage with Bactopia Tools |
| `bactopia-pubmlst-setup` | One-time setup for interacting with the PubMLST API |
| `bactopia-pubmlst-build` | Build PubMLST databases for use with the 'mlst' Bactopia Tool. |
Below is the `--help` output for each subcommand.
### `bactopia-citations`
```{bash}
Usage: bactopia-citations [OPTIONS]
Print out tools and citations used throughout Bactopia
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ --version -V Show the version and exit. │
│ * --bactopia-path -b TEXT Directory where Bactopia repository is stored │
│ [required] │
│ --name -n TEXT Only print citation matching a given name │
│ --plain-text -p Disable rich formatting │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
```
### `bactopia-datasets`
```{bash}
Usage: bactopia-datasets [OPTIONS] [UNKNOWN]...
Download optional datasets to supplement your analyses with Bactopia
╭─ Required Options ───────────────────────────────────────────────────────────────────╮
│ * --bactopia-path TEXT Directory where Bactopia repository is stored [required] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Download Related Options ───────────────────────────────────────────────────────────╮
│ --datasets_cache TEXT Base directory to download datasets to (Defaults to env │
│ variable BACTOPIA_CACHEDIR, a subfolder called datasets │
│ will be created) │
│ [default: ${HOME}/.bactopia] │
│ --force Force overwrite of existing pre-built environments. │
│ --max_retry INTEGER Maximum times to attempt creating Conda environment. │
│ (Default: 3) │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ─────────────────────────────────────────────────────────────────╮
│ --verbose Print debug related text. │
│ --silent Only critical errors will be printed. │
│ --version Show the version and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
```
### `bactopia-download`
```{bash}
Usage: bactopia-download [OPTIONS] [UNKNOWN]...
Builds Bactopia environments for use with Nextflow.
╭─ Required Options ───────────────────────────────────────────────────────────────────╮
│ * --bactopia-path TEXT Directory where Bactopia results are stored [required] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Build Related Options ──────────────────────────────────────────────────────────────╮
│ --envtype [conda|docker|singularity| The type of environment to │
│ all] build. │
│ [default: conda] │
│ --wf TEXT Build a environment for a │
│ the given workflow │
│ [default: bactopia] │
│ --condadir TEXT Directory to create Conda │
│ environments │
│ (NXF_CONDA_CACHEDIR env │
│ variable takes precedence) │
│ --use_conda Use Conda for building │
│ Conda environments instead │
│ of Mamba │
│ --singularity_cache TEXT Directory to download │
│ Singularity images │
│ (NXF_SINGULARITY_CACHEDIR │
│ env variable takes │
│ precedence) │
│ --singularity_pull_docker… Force conversion of Docker │
│ containers, instead │
│ downloading Singularity │
│ images directly │
│ --force_rebuild Force overwrite of │
│ existing pre-built │
│ environments. │
│ --max_retry INTEGER Maximum times to attempt │
│ creating Conda │
│ environment. (Default: 3) │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ─────────────────────────────────────────────────────────────────╮
│ --verbose Print debug related text. │
│ --silent Only critical errors will be printed. │
│ --version Show the version and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────────────╮
│ --build-all Builds all environments for Bactopia workflows │
│ --build-nfcore Builds all nf-core related environments │
╰──────────────────────────────────────────────────────────────────────────────────────╯
```
### `bactopia-prepare`
```{bash}
Usage: bactopia-prepare [OPTIONS]
Create a 'file of filenames' (FOFN) of samples to be processed by Bactopia
╭─ Required Options ───────────────────────────────────────────────────────────────────╮
│ * --path -p TEXT Directory where FASTQ files are stored [required] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Matching Options ───────────────────────────────────────────────────────────────────╮
│ --assembly-ext -a TEXT Extension of the FASTA assemblies [default: .fna.gz] │
│ --fastq-ext -f TEXT Extension of the FASTQs [default: .fastq.gz] │
│ --fastq-separator TEXT Split FASTQ name on the last occurrence of the │
│ separator │
│ [default: _] │
│ --pe1-pattern TEXT Designates difference first set of paired-end reads │
│ [default: [Aa]|[Rr]1|1] │
│ --pe2-pattern TEXT Designates difference second set of paired-end reads │
│ [default: [Bb]|[Rr]2|2] │
│ --merge Flag samples with multiple read sets to be merged by │
│ Bactopia │
│ --ont Single-end reads should be treated as Oxford Nanopore │
│ reads │
│ --recursive -r Directories will be traversed recursively │
│ --prefix TEXT Prefix to add to the path │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Sample Information Options ─────────────────────────────────────────────────────────╮
│ --metadata TEXT Metadata per sample with genome size and species │
│ information │
│ --genome-size -gsize INTEGER Genome size to use for all samples │
│ --species -s TEXT Species to use for all samples (If available, can be │
│ used to determine genome size) │
│ --taxid TEXT Use the genome size of the Taxon ID for all samples │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ─────────────────────────────────────────────────────────────────╮
│ --examples Print example usage │
│ --verbose Increase the verbosity of output │
│ --silent Only critical errors will be printed │
│ --version -V Show the version and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
```
### `bactopia-search`
```{bash}
Usage: bactopia-search [OPTIONS]
Query against ENA and SRA for public accessions to process with Bactopia
╭─ Required Options ───────────────────────────────────────────────────────────────────╮
│ * --query -q TEXT Taxon ID or Study, BioSample, or Run accession (can also be │
│ comma separated or a file of accessions) │
│ [required] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Query Options ──────────────────────────────────────────────────────────────────────╮
│ --exact-taxon Exclude Taxon ID descendants │
│ --limit -l INTEGER Maximum number of results (per query) to return │
│ [default: 1000000] │
│ --accession-limit -al INTEGER Maximum number of accessions to query at once │
│ [default: 5000] │
│ --biosample-subset INTEGER If a BioSample has multiple Experiments, maximum │
│ number to randomly select (0 = disabled) │
│ [default: 0] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Filtering Options ──────────────────────────────────────────────────────────────────╮
│ --min-base-count -mbc INTEGER Filters samples based on minimum base pair count │
│ (0 = disabled) │
│ [default: 0] │
│ --min-read-length -mrl INTEGER Filters samples based on minimum mean read length │
│ (0 = disabled) │
│ [default: 0] │
│ --min-coverage -mc INTEGER Filter samples based on minimum coverage (requires │
│ --genome_size, 0 = disabled) │
│ [default: 0] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ─────────────────────────────────────────────────────────────────╮
│ --genome-size -gsize INTEGER Genome size to be used for all samples, and for │
│ calculating min coverage │
│ [default: 0] │
│ --outdir -o TEXT Directory to write output [default: ./] │
│ --prefix -p TEXT Prefix to use for output file names │
│ [default: bactopia] │
│ --force Overwrite existing reports │
│ --verbose Increase the verbosity of output │
│ --silent Only critical errors will be printed │
│ --version -V Show the version and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
```
### `bactopia-summary`
```{bash}
Usage: bactopia-summary [OPTIONS]
Generate a summary table from the Bactopia results.
╭─ Required Options ───────────────────────────────────────────────────────────────────╮
│ * --bactopia-path -b TEXT Directory where Bactopia results are stored [required] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Gold Cutoffs ───────────────────────────────────────────────────────────────────────╮
│ --gold-coverage -gcov INTEGER Minimum amount of coverage required for Gold │
│ status │
│ [default: 100] │
│ --gold-quality -gqual INTEGER Minimum per-read mean quality score required │
│ for Gold status │
│ [default: 30] │
│ --gold-read-length -glen INTEGER Minimum mean read length required for Gold │
│ status │
│ [default: 95] │
│ --gold-contigs -gcontigs INTEGER Maximum contig count required for Gold │
│ status │
│ [default: 100] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Silver Cutoffs ─────────────────────────────────────────────────────────────────────╮
│ --silver-coverage -scov INTEGER Minimum amount of coverage required for │
│ Silver status │
│ [default: 50] │
│ --silver-quality -squal INTEGER Minimum per-read mean quality score │
│ required for Silver status │
│ [default: 20] │
│ --silver-read-length -slen INTEGER Minimum mean read length required for │
│ Silver status │
│ [default: 75] │
│ --silver-contigs -scontigs INTEGER Maximum contig count required for Silver │
│ status │
│ [default: 200] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Fail Cutoffs ───────────────────────────────────────────────────────────────────────╮
│ --min-coverage -mincov INTEGER Minimum amount of coverage required to pass │
│ [default: 20] │
│ --min-quality -minqual INTEGER Minimum per-read mean quality score │
│ required to pass │
│ [default: 12] │
│ --min-read-length -minlen INTEGER Minimum mean read length required to pass │
│ [default: 49] │
│ --max-contigs INTEGER Maximum contig count required to pass │
│ [default: 500] │
│ --min-assembled-size INTEGER Minimum assembled genome size │
│ --max-assembled-size INTEGER Maximum assembled genome size │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ─────────────────────────────────────────────────────────────────╮
│ --outdir -o PATH Directory to write output [default: ./] │
│ --prefix -p TEXT Prefix to use for output files [default: bactopia] │
│ --force Overwrite existing reports │
│ --verbose Increase the verbosity of output │
│ --silent Only critical errors will be printed │
│ --version -V Show the version and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
```
# All The Bacteria (ATB)
The [AllTheBacteria](https://www.biorxiv.org/content/10.1101/2024.03.08.584059v1) is a collection
of nearly 2,000,000 bacterial genomes. Using available FASTQ files from the European Nucleotide
Archive (ENA) and Sequence Read Archive (SRA), the genomes were assembled using [Shovill] and made
publicly available from the [Iqbal Lab](https://github.com/iqbal-lab-org/AllTheBacteria).
To make it easy to utilize [Bactopia Tools](https://bactopia.github.io/latest/bactopia-tools/) with
assemblies from AllTheBacteria, `bactopia-atb-formatter` was created. This tool will create a
directory structure that resembles output from an actual Bactopia run.
### `bactopia-atb-formatter`
```{bash}
Usage: bactopia-atb-formatter [OPTIONS]
Restructure All-the-Bacteria assemblies to allow usage with Bactopia Tools
╭─ Required Options ───────────────────────────────────────────────────────────────────╮
│ * --path -p TEXT Directory where FASTQ files are stored [required] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Bactopia Directory Structure Options ───────────────────────────────────────────────╮
│ --bactopia-dir -b TEXT The path you would like to place bactopia │
│ structure │
│ [default: bactopia] │
│ --publish-mode -m [symlink|copy] Designates plascement of assemblies will be │
│ handled │
│ [default: symlink] │
│ --recursive -r Traverse recursively through provided path │
│ --extension -e TEXT The extension of the assemblies e.g .fa,.fa.gz │
│ [default: .fa] │
╰──────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ─────────────────────────────────────────────────────────────────╮
│ --verbose Increase the verbosity of output │
│ --silent Only critical errors will be printed │
│ --version -V Show the version and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────╯
```
### Example Usage for _Legionella pneumophila_
To demonstrate the usage of `bactopia-atb-formatter`, we will use assemblies for
_Legionella pneumophila_. The following steps will download the assemblies, build the
Bactopia directory structure, and then run [legsta](https://github.com/tseemann/legsta)
via the [Bactopia Tool](https://bactopia.github.io/latest/bactopia-tools/legsta/).
#### Download the Assemblies
First will download the _Legionella pneumophila_ assemblies from AllTheBacteria. After downloading
we will extract them into a folder called `legionella-assemblies`. Within this folder, there will be
subdirectories for each tarball that was downloaded.
```{bash}
mkdir atb-legionella
cd atb-legionella
# Download the assemblies
wget https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.1/assembly/legionella_pneumophila__01.asm.tar.xz
wget https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.1/assembly/legionella_pneumophila__02.asm.tar.xz
# Extract the assemblies
mkdir legionella-assemblies
tar -C legionella-assemblies -xJf legionella_pneumophila__01.asm.tar.xz
tar -C legionella-assemblies -xJf legionella_pneumophila__02.asm.tar.xz
```
#### Create the Bactopia Directory Structure
With the assemblies extracted, we can now create the Bactopia directory structure using
`bactopia-atb-formatter`. Once complete, each assembly will have its own folder created
which matches the BioSample accession of the assembly.
```{bash}
# Create the Bactopia directory structure
bactopia atb-formatter --path legionella-assemblies --recursive
2024-03-22 14:30:07 INFO 2024-03-22 14:30:07:root:INFO - Setting up Bactopia directory structure (use --verbose to see more details) atb_formatter.py:129
2024-03-22 14:30:08 INFO 2024-03-22 14:30:08:root:INFO - Bactopia directory structure created at bactopia atb_formatter.py:134
INFO 2024-03-22 14:30:08:root:INFO - Total assemblies processed: 5393
```
Please note the usage of `--recursive` which will traverse the `legionella-assemblies` directory
to find all assemblies contained. At this point, the `bactopia` directory structure has been
created for 5,393 assemblies and is ready for use with Bactopia Tools.
#### Use Bactopia to run Legsta
As mentioned above, we will use [legsta](https://github.com/tseemann/legsta) to analyze each
of the _Legionella pneumophila_ assemblies. To do this, we will use the
[legsta Bactopia Tool](https://bactopia.github.io/latest/bactopia-tools/legsta/).
```{bash}
# Run legsta (please utilize Docker or Singularity only for reproducibility)
bactopia --wf legsta -profile singularity
```
Please note, for reproducibility, it is recommended to use Docker or Singularity with
Bactopia Tools.
Upon completion, you should be met with something like the following:
```{bash}
[5d/d04297] process > BACTOPIATOOLS:LEGSTA:LEGSTA_MODULE (SAMN29911258) [100%] 5393 of 5393 ✔
[71/c63bf7] process > BACTOPIATOOLS:LEGSTA:CSVTK_CONCAT (legsta) [100%] 1 of 1 ✔
[16/833262] process > BACTOPIATOOLS:CUSTOM_DUMPSOFTWAREVERSIONS (1) [100%] 1 of 1 ✔
Bactopia Tools: `legsta Execution Summary
---------------------------
Bactopia Version : 3.0.1
Nextflow Version : 23.10.1
Command Line : nextflow run /home/rpetit3/bactopia/main.nf --wf legsta --bactopia bactopia/ -profile singularity
Resumed : false
Completed At : 2024-03-22T15:09:54.959834620-06:00
Duration : 32m 51s
Success : true
Exit Code : 0
Error Report : -
Launch Dir : /home/rpetit3/test-legsta
WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info.
Completed at: 22-Mar-2024 15:09:55
Duration : 32m 52s
CPU hours : 5.2
Succeeded : 5'395
```
That's it! Now you can take advantage of any of the [Bactopia Tools](https://bactopia.github.io/latest/bactopia-tools/)
that utilize assemblies as inputs.
# PubMLST DB Builds
As of [v1.4.0](https://github.com/bactopia/bactopia-py/releases/tag/v1.4.0), `bactopia-py` now includes commands
(`bactopia-pubmlst-setup` and `bactopia-pubmlst-build`) to help you build PubMLST databases using their RestAPI,
instead of the XML files. By using the RestAPI, you will always retrieve the latest schema and allele information
for all available organisms (_the XML build did not include all organisms_).
One thing to note, its by using the RestAPI, there is a one time manual process of setting up the necessary credentials.
No worries, though, `bactopia-pubmlst-setup` will assist you with this process.
## `bactopia-pubmlst-setup`
The first step of building PubMLST databases is to setup your credentials. Due to the way the PubMLST API works, you
will need to do this interactively. In order to make this work you will need already have created an account on the
PubMLST website, then created a client ID and client secret. To learn more about this process, please visit the
[PubMLST API Authentication Docs](https://bigsdb.readthedocs.io/en/latest/rest.html#authentication).
Once you have your client ID and client secret, you can run `bactopia-pubmlst-setup` to setup your credentials.
```{bash}
Usage: bactopia-pubmlst-setup [OPTIONS]
One-time setup for interacting with the PubMLST API
╭─ Required Options ──────────────────────────────────────────────────────────────────╮
│ * --client-id -ci TEXT The client ID for the site [required] │
│ * --client-secret -cs TEXT The client secret for the site [required] │
╰─────────────────────────────────────────────────────────────────────────────────────╯
╭─ API Options ───────────────────────────────────────────────────────────────────────╮
│ --site -s [pubmlst|pasteur] Only print citation matching a given name │
│ [default: pubmlst] │
│ --database -d TEXT The organism database to interact with for │
│ setup. Note: the default is available from both │
│ PubMLST and Pasteur │
│ [default: pubmlst_yersinia_seqdef] │
│ --save-dir -sd TEXT The directory to save the token │
│ [default: /home/gitpod/.bactopia] │
│ --force Force overwrite of existing token files. │
╰─────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ────────────────────────────────────────────────────────────────╮
│ --verbose Print debug related text. │
│ --silent Only critical errors will be printed. │
│ --version -V Show the version and exit. │
│ --help Show this message and exit. │
╰─────────────────────────────────────────────────────────────────────────────────────╯
```
## `bactopia-pubmlst-build`
The `bactopia-pubmlst-build` command will build MLST databases for a given organism or all available organisms. In order
utilize this command you will need to have already setup your credentials using `bactopia-pubmlst-setup`.
```{bash}
Usage: bactopia-pubmlst-build [OPTIONS]
Build PubMLST databases for use with the 'mlst' Bactopia Tool.
╭─ Required Options ──────────────────────────────────────────────────────────────────╮
│ --database -d TEXT A known organism database to download. (Use 'all' to download │
│ all databases.) │
╰─────────────────────────────────────────────────────────────────────────────────────╯
╭─ Build Options ─────────────────────────────────────────────────────────────────────╮
│ --ignore TEXT A comma separated list of databases to ignore. │
│ [default: │
│ afumigatus,blastocystis,calbicans,cbotulinum,cglabrata,ck… │
│ --skip-download Skip downloading the database files. │
│ --skip-blast Skip building the BLAST database. │
│ --force Force overwrite of existing files. │
╰─────────────────────────────────────────────────────────────────────────────────────╯
╭─ API Options ───────────────────────────────────────────────────────────────────────╮
│ --site -s [pubmlst|pasteur] Only print citation matching a given name │
│ [default: pubmlst] │
│ --token-dir -t TEXT The directory where the token file is saved. │
│ [default: /home/gitpod/.bactopia] │
│ --out-dir -o TEXT The directory where the database files will be │
│ saved. │
│ [default: ./bactopia-mlst] │
╰─────────────────────────────────────────────────────────────────────────────────────╯
╭─ Additional Options ────────────────────────────────────────────────────────────────╮
│ --verbose Print debug related text. │
│ --silent Only critical errors will be printed. │
│ --version -V Show the version and exit. │
│ --help Show this message and exit. │
╰─────────────────────────────────────────────────────────────────────────────────────╯
```
# Feedback
Your feedback is very valuable! If you run into any issues using Bactopia, have questions, or have some ideas to improve Bactopia, I highly encourage you to submit it to the [Issue Tracker](https://github.com/bactopia/bactopia/issues).
# License
[MIT License](https://raw.githubusercontent.com/bactopia/bactopia/master/LICENSE)
# Citation
Petit III RA, Read TD, *Bactopia: a flexible pipeline for complete analysis of bacterial genomes.* __mSystems__. 5 (2020), https://doi.org/10.1128/mSystems.00190-20.
# Author
* Robert A. Petit III
* Twitter: [@rpetit3](https://twitter.com/rpetit3)
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"description": "[](https://gitpod.io/#https://github.com/bactopia/bactopia-py)\n\n\n\n# bactopia-py\nA Python package for working with [Bactopia](https://bactopia.github.io/)\n\n## Bactopia Subcommands\n\nThere are many subcommands available in Bactopia. Here is a brief description of each command:\n\n| Command | Description |\n|---------------------------|----------------------------------------------------------------------------|\n| `bactopia-citations` | Print out tools and citations used throughout Bactopia |\n| `bactopia-datasets` | Download optional datasets to supplement your analyses with Bactopia |\n| `bactopia-download` | Builds Bactopia environments for use with Nextflow. |\n| `bactopia-prepare` | Create a 'file of filenames' (FOFN) of samples to be processed by Bactopia |\n| `bactopia-search` | Query against ENA and SRA for public accessions to process with Bactopia |\n| `bactopia-summary` | Generate a summary table from the Bactopia results. |\n| `bactopia-atb-downloader` | Download assemblies from AllTheBacteria for use with Bactopia Tools |\n| `bactopia-atb-formatter` | Restructure All-the-Bacteria assemblies to allow usage with Bactopia Tools |\n| `bactopia-pubmlst-setup` | One-time setup for interacting with the PubMLST API |\n| `bactopia-pubmlst-build` | Build PubMLST databases for use with the 'mlst' Bactopia Tool. |\n\nBelow is the `--help` output for each subcommand.\n\n### `bactopia-citations`\n\n```{bash}\n Usage: bactopia-citations [OPTIONS]\n\n Print out tools and citations used throughout Bactopia\n\n\u256d\u2500 Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --version -V Show the version and exit. \u2502\n\u2502 * --bactopia-path -b TEXT Directory where Bactopia repository is stored \u2502\n\u2502 [required] \u2502\n\u2502 --name -n TEXT Only print citation matching a given name \u2502\n\u2502 --plain-text -p Disable rich formatting \u2502\n\u2502 --help Show this message and exit. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\n### `bactopia-datasets`\n\n```{bash}\n Usage: bactopia-datasets [OPTIONS] [UNKNOWN]...\n\n Download optional datasets to supplement your analyses with Bactopia\n\n\u256d\u2500 Required Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 * --bactopia-path TEXT Directory where Bactopia repository is stored [required] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Download Related Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --datasets_cache TEXT Base directory to download datasets to (Defaults to env \u2502\n\u2502 variable BACTOPIA_CACHEDIR, a subfolder called datasets \u2502\n\u2502 will be created) \u2502\n\u2502 [default: ${HOME}/.bactopia] \u2502\n\u2502 --force Force overwrite of existing pre-built environments. \u2502\n\u2502 --max_retry INTEGER Maximum times to attempt creating Conda environment. \u2502\n\u2502 (Default: 3) \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Additional Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --verbose Print debug related text. \u2502\n\u2502 --silent Only critical errors will be printed. \u2502\n\u2502 --version Show the version and exit. \u2502\n\u2502 --help Show this message and exit. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\n```\n\n### `bactopia-download`\n\n```{bash}\n Usage: bactopia-download [OPTIONS] [UNKNOWN]...\n\n Builds Bactopia environments for use with Nextflow.\n\n\u256d\u2500 Required Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 * --bactopia-path TEXT Directory where Bactopia results are stored [required] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Build Related Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --envtype [conda|docker|singularity| The type of environment to \u2502\n\u2502 all] build. \u2502\n\u2502 [default: conda] \u2502\n\u2502 --wf TEXT Build a environment for a \u2502\n\u2502 the given workflow \u2502\n\u2502 [default: bactopia] \u2502\n\u2502 --condadir TEXT Directory to create Conda \u2502\n\u2502 environments \u2502\n\u2502 (NXF_CONDA_CACHEDIR env \u2502\n\u2502 variable takes precedence) \u2502\n\u2502 --use_conda Use Conda for building \u2502\n\u2502 Conda environments instead \u2502\n\u2502 of Mamba \u2502\n\u2502 --singularity_cache TEXT Directory to download \u2502\n\u2502 Singularity images \u2502\n\u2502 (NXF_SINGULARITY_CACHEDIR \u2502\n\u2502 env variable takes \u2502\n\u2502 precedence) \u2502\n\u2502 --singularity_pull_docker\u2026 Force conversion of Docker \u2502\n\u2502 containers, instead \u2502\n\u2502 downloading Singularity \u2502\n\u2502 images directly \u2502\n\u2502 --force_rebuild Force overwrite of \u2502\n\u2502 existing pre-built \u2502\n\u2502 environments. \u2502\n\u2502 --max_retry INTEGER Maximum times to attempt \u2502\n\u2502 creating Conda \u2502\n\u2502 environment. (Default: 3) \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Additional Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --verbose Print debug related text. \u2502\n\u2502 --silent Only critical errors will be printed. \u2502\n\u2502 --version Show the version and exit. \u2502\n\u2502 --help Show this message and exit. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --build-all Builds all environments for Bactopia workflows \u2502\n\u2502 --build-nfcore Builds all nf-core related environments \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\n### `bactopia-prepare`\n\n```{bash}\n Usage: bactopia-prepare [OPTIONS]\n\n Create a 'file of filenames' (FOFN) of samples to be processed by Bactopia\n\n\u256d\u2500 Required Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 * --path -p TEXT Directory where FASTQ files are stored [required] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Matching Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --assembly-ext -a TEXT Extension of the FASTA assemblies [default: .fna.gz] \u2502\n\u2502 --fastq-ext -f TEXT Extension of the FASTQs [default: .fastq.gz] \u2502\n\u2502 --fastq-separator TEXT Split FASTQ name on the last occurrence of the \u2502\n\u2502 separator \u2502\n\u2502 [default: _] \u2502\n\u2502 --pe1-pattern TEXT Designates difference first set of paired-end reads \u2502\n\u2502 [default: [Aa]|[Rr]1|1] \u2502\n\u2502 --pe2-pattern TEXT Designates difference second set of paired-end reads \u2502\n\u2502 [default: [Bb]|[Rr]2|2] \u2502\n\u2502 --merge Flag samples with multiple read sets to be merged by \u2502\n\u2502 Bactopia \u2502\n\u2502 --ont Single-end reads should be treated as Oxford Nanopore \u2502\n\u2502 reads \u2502\n\u2502 --recursive -r Directories will be traversed recursively \u2502\n\u2502 --prefix TEXT Prefix to add to the path \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Sample Information Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --metadata TEXT Metadata per sample with genome size and species \u2502\n\u2502 information \u2502\n\u2502 --genome-size -gsize INTEGER Genome size to use for all samples \u2502\n\u2502 --species -s TEXT Species to use for all samples (If available, can be \u2502\n\u2502 used to determine genome size) \u2502\n\u2502 --taxid TEXT Use the genome size of the Taxon ID for all samples \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Additional Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --examples Print example usage \u2502\n\u2502 --verbose Increase the verbosity of output \u2502\n\u2502 --silent Only critical errors will be printed \u2502\n\u2502 --version -V Show the version and exit. \u2502\n\u2502 --help Show this message and exit. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\n### `bactopia-search`\n\n```{bash}\n Usage: bactopia-search [OPTIONS]\n\n Query against ENA and SRA for public accessions to process with Bactopia\n\n\u256d\u2500 Required Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 * --query -q TEXT Taxon ID or Study, BioSample, or Run accession (can also be \u2502\n\u2502 comma separated or a file of accessions) \u2502\n\u2502 [required] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Query Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --exact-taxon Exclude Taxon ID descendants \u2502\n\u2502 --limit -l INTEGER Maximum number of results (per query) to return \u2502\n\u2502 [default: 1000000] \u2502\n\u2502 --accession-limit -al INTEGER Maximum number of accessions to query at once \u2502\n\u2502 [default: 5000] \u2502\n\u2502 --biosample-subset INTEGER If a BioSample has multiple Experiments, maximum \u2502\n\u2502 number to randomly select (0 = disabled) \u2502\n\u2502 [default: 0] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Filtering Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --min-base-count -mbc INTEGER Filters samples based on minimum base pair count \u2502\n\u2502 (0 = disabled) \u2502\n\u2502 [default: 0] \u2502\n\u2502 --min-read-length -mrl INTEGER Filters samples based on minimum mean read length \u2502\n\u2502 (0 = disabled) \u2502\n\u2502 [default: 0] \u2502\n\u2502 --min-coverage -mc INTEGER Filter samples based on minimum coverage (requires \u2502\n\u2502 --genome_size, 0 = disabled) \u2502\n\u2502 [default: 0] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Additional Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --genome-size -gsize INTEGER Genome size to be used for all samples, and for \u2502\n\u2502 calculating min coverage \u2502\n\u2502 [default: 0] \u2502\n\u2502 --outdir -o TEXT Directory to write output [default: ./] \u2502\n\u2502 --prefix -p TEXT Prefix to use for output file names \u2502\n\u2502 [default: bactopia] \u2502\n\u2502 --force Overwrite existing reports \u2502\n\u2502 --verbose Increase the verbosity of output \u2502\n\u2502 --silent Only critical errors will be printed \u2502\n\u2502 --version -V Show the version and exit. \u2502\n\u2502 --help Show this message and exit. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\n### `bactopia-summary`\n\n```{bash}\n Usage: bactopia-summary [OPTIONS]\n\n Generate a summary table from the Bactopia results.\n\n\u256d\u2500 Required Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 * --bactopia-path -b TEXT Directory where Bactopia results are stored [required] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Gold Cutoffs \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --gold-coverage -gcov INTEGER Minimum amount of coverage required for Gold \u2502\n\u2502 status \u2502\n\u2502 [default: 100] \u2502\n\u2502 --gold-quality -gqual INTEGER Minimum per-read mean quality score required \u2502\n\u2502 for Gold status \u2502\n\u2502 [default: 30] \u2502\n\u2502 --gold-read-length -glen INTEGER Minimum mean read length required for Gold \u2502\n\u2502 status \u2502\n\u2502 [default: 95] \u2502\n\u2502 --gold-contigs -gcontigs INTEGER Maximum contig count required for Gold \u2502\n\u2502 status \u2502\n\u2502 [default: 100] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Silver Cutoffs \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --silver-coverage -scov INTEGER Minimum amount of coverage required for \u2502\n\u2502 Silver status \u2502\n\u2502 [default: 50] \u2502\n\u2502 --silver-quality -squal INTEGER Minimum per-read mean quality score \u2502\n\u2502 required for Silver status \u2502\n\u2502 [default: 20] \u2502\n\u2502 --silver-read-length -slen INTEGER Minimum mean read length required for \u2502\n\u2502 Silver status \u2502\n\u2502 [default: 75] \u2502\n\u2502 --silver-contigs -scontigs INTEGER Maximum contig count required for Silver \u2502\n\u2502 status \u2502\n\u2502 [default: 200] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Fail Cutoffs \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --min-coverage -mincov INTEGER Minimum amount of coverage required to pass \u2502\n\u2502 [default: 20] \u2502\n\u2502 --min-quality -minqual INTEGER Minimum per-read mean quality score \u2502\n\u2502 required to pass \u2502\n\u2502 [default: 12] \u2502\n\u2502 --min-read-length -minlen INTEGER Minimum mean read length required to pass \u2502\n\u2502 [default: 49] \u2502\n\u2502 --max-contigs INTEGER Maximum contig count required to pass \u2502\n\u2502 [default: 500] \u2502\n\u2502 --min-assembled-size INTEGER Minimum assembled genome size \u2502\n\u2502 --max-assembled-size INTEGER Maximum assembled genome size \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Additional Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --outdir -o PATH Directory to write output [default: ./] \u2502\n\u2502 --prefix -p TEXT Prefix to use for output files [default: bactopia] \u2502\n\u2502 --force Overwrite existing reports \u2502\n\u2502 --verbose Increase the verbosity of output \u2502\n\u2502 --silent Only critical errors will be printed \u2502\n\u2502 --version -V Show the version and exit. \u2502\n\u2502 --help Show this message and exit. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\n# All The Bacteria (ATB)\n\nThe [AllTheBacteria](https://www.biorxiv.org/content/10.1101/2024.03.08.584059v1) is a collection\nof nearly 2,000,000 bacterial genomes. Using available FASTQ files from the European Nucleotide\nArchive (ENA) and Sequence Read Archive (SRA), the genomes were assembled using [Shovill] and made\npublicly available from the [Iqbal Lab](https://github.com/iqbal-lab-org/AllTheBacteria).\n\nTo make it easy to utilize [Bactopia Tools](https://bactopia.github.io/latest/bactopia-tools/) with\nassemblies from AllTheBacteria, `bactopia-atb-formatter` was created. This tool will create a \ndirectory structure that resembles output from an actual Bactopia run.\n\n### `bactopia-atb-formatter`\n\n```{bash}\n Usage: bactopia-atb-formatter [OPTIONS]\n\n Restructure All-the-Bacteria assemblies to allow usage with Bactopia Tools\n\n\u256d\u2500 Required Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 * --path -p TEXT Directory where FASTQ files are stored [required] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Bactopia Directory Structure Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --bactopia-dir -b TEXT The path you would like to place bactopia \u2502\n\u2502 structure \u2502\n\u2502 [default: bactopia] \u2502\n\u2502 --publish-mode -m [symlink|copy] Designates plascement of assemblies will be \u2502\n\u2502 handled \u2502\n\u2502 [default: symlink] \u2502\n\u2502 --recursive -r Traverse recursively through provided path \u2502\n\u2502 --extension -e TEXT The extension of the assemblies e.g .fa,.fa.gz \u2502\n\u2502 [default: .fa] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Additional Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --verbose Increase the verbosity of output \u2502\n\u2502 --silent Only critical errors will be printed \u2502\n\u2502 --version -V Show the version and exit. \u2502\n\u2502 --help Show this message and exit. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\n### Example Usage for _Legionella pneumophila_\n\nTo demonstrate the usage of `bactopia-atb-formatter`, we will use assemblies for\n_Legionella pneumophila_. The following steps will download the assemblies, build the\nBactopia directory structure, and then run [legsta](https://github.com/tseemann/legsta)\nvia the [Bactopia Tool](https://bactopia.github.io/latest/bactopia-tools/legsta/).\n\n#### Download the Assemblies\n\nFirst will download the _Legionella pneumophila_ assemblies from AllTheBacteria. After downloading\nwe will extract them into a folder called `legionella-assemblies`. Within this folder, there will be\nsubdirectories for each tarball that was downloaded.\n\n```{bash}\nmkdir atb-legionella\ncd atb-legionella\n\n# Download the assemblies\nwget https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.1/assembly/legionella_pneumophila__01.asm.tar.xz\nwget https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.1/assembly/legionella_pneumophila__02.asm.tar.xz\n\n# Extract the assemblies\nmkdir legionella-assemblies\ntar -C legionella-assemblies -xJf legionella_pneumophila__01.asm.tar.xz\ntar -C legionella-assemblies -xJf legionella_pneumophila__02.asm.tar.xz\n```\n\n#### Create the Bactopia Directory Structure\n\nWith the assemblies extracted, we can now create the Bactopia directory structure using\n`bactopia-atb-formatter`. Once complete, each assembly will have its own folder created\nwhich matches the BioSample accession of the assembly.\n\n```{bash}\n# Create the Bactopia directory structure\nbactopia atb-formatter --path legionella-assemblies --recursive\n2024-03-22 14:30:07 INFO 2024-03-22 14:30:07:root:INFO - Setting up Bactopia directory structure (use --verbose to see more details) atb_formatter.py:129\n2024-03-22 14:30:08 INFO 2024-03-22 14:30:08:root:INFO - Bactopia directory structure created at bactopia atb_formatter.py:134\n INFO 2024-03-22 14:30:08:root:INFO - Total assemblies processed: 5393\n```\n\nPlease note the usage of `--recursive` which will traverse the `legionella-assemblies` directory\nto find all assemblies contained. At this point, the `bactopia` directory structure has been\ncreated for 5,393 assemblies and is ready for use with Bactopia Tools.\n\n#### Use Bactopia to run Legsta\n\nAs mentioned above, we will use [legsta](https://github.com/tseemann/legsta) to analyze each\nof the _Legionella pneumophila_ assemblies. To do this, we will use the\n[legsta Bactopia Tool](https://bactopia.github.io/latest/bactopia-tools/legsta/).\n\n```{bash}\n# Run legsta (please utilize Docker or Singularity only for reproducibility)\nbactopia --wf legsta -profile singularity\n```\n\nPlease note, for reproducibility, it is recommended to use Docker or Singularity with\nBactopia Tools.\n\nUpon completion, you should be met with something like the following:\n\n```{bash}\n[5d/d04297] process > BACTOPIATOOLS:LEGSTA:LEGSTA_MODULE (SAMN29911258) [100%] 5393 of 5393 \u2714\n[71/c63bf7] process > BACTOPIATOOLS:LEGSTA:CSVTK_CONCAT (legsta) [100%] 1 of 1 \u2714\n[16/833262] process > BACTOPIATOOLS:CUSTOM_DUMPSOFTWAREVERSIONS (1) [100%] 1 of 1 \u2714\n\n Bactopia Tools: `legsta Execution Summary\n ---------------------------\n Bactopia Version : 3.0.1\n Nextflow Version : 23.10.1\n Command Line : nextflow run /home/rpetit3/bactopia/main.nf --wf legsta --bactopia bactopia/ -profile singularity\n Resumed : false\n Completed At : 2024-03-22T15:09:54.959834620-06:00\n Duration : 32m 51s\n Success : true\n Exit Code : 0\n Error Report : -\n Launch Dir : /home/rpetit3/test-legsta\n\nWARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info.\nCompleted at: 22-Mar-2024 15:09:55\nDuration : 32m 52s\nCPU hours : 5.2\nSucceeded : 5'395\n```\n\nThat's it! Now you can take advantage of any of the [Bactopia Tools](https://bactopia.github.io/latest/bactopia-tools/)\nthat utilize assemblies as inputs.\n\n# PubMLST DB Builds\n\nAs of [v1.4.0](https://github.com/bactopia/bactopia-py/releases/tag/v1.4.0), `bactopia-py` now includes commands\n(`bactopia-pubmlst-setup` and `bactopia-pubmlst-build`) to help you build PubMLST databases using their RestAPI,\ninstead of the XML files. By using the RestAPI, you will always retrieve the latest schema and allele information\nfor all available organisms (_the XML build did not include all organisms_).\n\nOne thing to note, its by using the RestAPI, there is a one time manual process of setting up the necessary credentials.\nNo worries, though, `bactopia-pubmlst-setup` will assist you with this process.\n\n## `bactopia-pubmlst-setup`\n\nThe first step of building PubMLST databases is to setup your credentials. Due to the way the PubMLST API works, you\nwill need to do this interactively. In order to make this work you will need already have created an account on the\nPubMLST website, then created a client ID and client secret. To learn more about this process, please visit the\n[PubMLST API Authentication Docs](https://bigsdb.readthedocs.io/en/latest/rest.html#authentication).\n\nOnce you have your client ID and client secret, you can run `bactopia-pubmlst-setup` to setup your credentials.\n\n```{bash}\n \n Usage: bactopia-pubmlst-setup [OPTIONS] \n \n One-time setup for interacting with the PubMLST API \n \n\u256d\u2500 Required Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 * --client-id -ci TEXT The client ID for the site [required] \u2502\n\u2502 * --client-secret -cs TEXT The client secret for the site [required] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 API Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --site -s [pubmlst|pasteur] Only print citation matching a given name \u2502\n\u2502 [default: pubmlst] \u2502\n\u2502 --database -d TEXT The organism database to interact with for \u2502\n\u2502 setup. Note: the default is available from both \u2502\n\u2502 PubMLST and Pasteur \u2502\n\u2502 [default: pubmlst_yersinia_seqdef] \u2502\n\u2502 --save-dir -sd TEXT The directory to save the token \u2502\n\u2502 [default: /home/gitpod/.bactopia] \u2502\n\u2502 --force Force overwrite of existing token files. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Additional Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --verbose Print debug related text. \u2502\n\u2502 --silent Only critical errors will be printed. \u2502\n\u2502 --version -V Show the version and exit. \u2502\n\u2502 --help Show this message and exit. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\n## `bactopia-pubmlst-build`\n\nThe `bactopia-pubmlst-build` command will build MLST databases for a given organism or all available organisms. In order\nutilize this command you will need to have already setup your credentials using `bactopia-pubmlst-setup`.\n\n```{bash}\n \n Usage: bactopia-pubmlst-build [OPTIONS] \n \n Build PubMLST databases for use with the 'mlst' Bactopia Tool. \n \n\u256d\u2500 Required Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --database -d TEXT A known organism database to download. (Use 'all' to download \u2502\n\u2502 all databases.) \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Build Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --ignore TEXT A comma separated list of databases to ignore. \u2502\n\u2502 [default: \u2502\n\u2502 afumigatus,blastocystis,calbicans,cbotulinum,cglabrata,ck\u2026 \u2502\n\u2502 --skip-download Skip downloading the database files. \u2502\n\u2502 --skip-blast Skip building the BLAST database. \u2502\n\u2502 --force Force overwrite of existing files. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 API Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --site -s [pubmlst|pasteur] Only print citation matching a given name \u2502\n\u2502 [default: pubmlst] \u2502\n\u2502 --token-dir -t TEXT The directory where the token file is saved. \u2502\n\u2502 [default: /home/gitpod/.bactopia] \u2502\n\u2502 --out-dir -o TEXT The directory where the database files will be \u2502\n\u2502 saved. \u2502\n\u2502 [default: ./bactopia-mlst] \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n\u256d\u2500 Additional Options \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256e\n\u2502 --verbose Print debug related text. \u2502\n\u2502 --silent Only critical errors will be printed. \u2502\n\u2502 --version -V Show the version and exit. \u2502\n\u2502 --help Show this message and exit. \u2502\n\u2570\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u256f\n```\n\n# Feedback\nYour feedback is very valuable! If you run into any issues using Bactopia, have questions, or have some ideas to improve Bactopia, I highly encourage you to submit it to the [Issue Tracker](https://github.com/bactopia/bactopia/issues).\n\n# License\n[MIT License](https://raw.githubusercontent.com/bactopia/bactopia/master/LICENSE)\n\n# Citation\n\nPetit III RA, Read TD, *Bactopia: a flexible pipeline for complete analysis of bacterial genomes.* __mSystems__. 5 (2020), https://doi.org/10.1128/mSystems.00190-20.\n\n# Author\n\n* Robert A. Petit III\n* Twitter: [@rpetit3](https://twitter.com/rpetit3)\n\n",
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