[](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. |
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.
# 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\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# 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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