[](https://edwards.flinders.edu.au)
[](https://opensource.org/licenses/MIT)
[](https://github.com/beardymcjohnface/Snaketool)
[](https://github.com/npbhavya/baczy/actions/workflows/testing.yml)
# Baczy
<p align="center">
<img src="baczy.png#gh-light-mode-only" width="300">
<img src="baczy.png#gh-dark-mode-only" width="300">
</p>
## Overview
**Baczy** is a **Snakemake-based workflow** for **assembling and annotating bacterial host genomes**. It extends **[Sphae](https://github.com/linsalrob/sphae)**, which assembles and annotates phage genomes, by enabling host genome assembly and functional annotation.
🔹 **Features:**
✔ **Quality control** ([Fastp](https://github.com/OpenGene/fastp))
✔ **Genome assembly** ([MEGAHIT](https://github.com/voutcn/megahit), [Hybracter](https://github.com/gbouras13/hybracter))
✔ **Functional annotation** ([Bakta](https://github.com/oschwengers/bakta))
✔ **Taxonomic classification** ([GTDB-Tk](https://github.com/Ecogenomics/GTDBTk))
✔ **Taxonomic tree** ([GTDB-Tk](https://github.com/Ecogenomics/GTDBTk))
✔ **Defense & resistance profiling** ([Defense-Finder](https://github.com/mdmparis/defense-finder), [AMRFinderPlus](https://github.com/ncbi/amr), [CapsuleDB](https://research.pasteur.fr/en/tool/capsulefinder/))
✔ **Prophage detection** ([PhiSpy](https://github.com/linsalrob/PhiSpy))
✔ **Pan-genome analysis** ([Panaroo](https://github.com/gtonkinhill/panaroo))
## Installion
Steps for installing workflow
```bash
#clone repository
git clone https://github.com/npbhavya/baczy.git
#move to sphae folder
cd baczy
#install
pip install -e .
#confirm the workflow is installed by running the below command
baczy --help
```
### Manual installation
- Install singularity or load the module
On deepthought cluster \
`module load apptainer`
- Install miniconda
Download and install Miniconda:
[Miniconda Installation Guide](https://docs.anaconda.com/miniconda/install/)
## Database setup
Download and place the required databases in:
`baczy/workflow/databases`
- [CheckM2_database](https://github.com/chklovski/CheckM2?tab=readme-ov-file#database)
- [GTDBTK database](https://ecogenomics.github.io/GTDBTk/installing/index.html)
- [Capsuledb](https://gitlab.pasteur.fr/gem/capsuledb/-/tree/master/CapsuleFinder_models?ref_type=heads)
### Running the workflow
Run Baczy using a single command!
**Before starting the run**
The taxonomic tree is generated using [GTDB-Tk](https://github.com/Ecogenomics/GTDBTk), so update the lines
```
gtdbtk:
outgroup: "d__Archaea"
taxa_filter: "d__Bacteria"
```
This can be set to more specific genera:
```
gtdbtk:
outgroup: "g__Escherichia"
taxa_filter: "g__Achromobacter"
```
**For paired end reads**
`baczy run --input sample-data/illumina --cores 32 --use-singularity --sdm apptainer --output test -k --use-conda`
**For long reads**
`baczy run --input sample-data/nanopore --sequencing longread --cores 32 -k --use-singularity --sdm apptainer --output test -k --use-conda`
### Intermediate files
Stored in:
`baczy.out/PROCESSING`
### Final Results and Output
Stored in `RESULT-short` for short reads or `RESULTS-long` for long reads
Each folder contains:
- **{sample} folder**
- {sample}_amrfinderplus table: identified AMR genes in the genome
- {sample}_contigs.fa or {sample}_final.fasta : assembled genomes for each genome
- {sample}.faa : identified proteins
- {sample}.fna : identified genes
- {sample}.gbff
- {sample}.gff3
- {sample}.png and {sample}.svg : genome visualized
- {sample}.txt: summary
- {sample}_prophage_coordinates.tsv: location of the identified prophages using Phispy
- **amrfinder_summary.tsv** : a table with all the AMRFinder genes in all the samples
- **bakta_summary.tsv** : Bakta summary for all the samples saved to one table
- **checkm2_quality_report.tsv** : Checkm2 completenes results
- **defensefinder_summary.tsv** : All the defense systems found in all the samples
- **gtdbtk.ba120_summary.tsv** : GTDBTK summary with the predicted taxa for each of the samples
- **gtdbtk.bac120.decorated.tree** , *gtdbtk.bac120.tree.table* : GTDBTK tree and the tree table
- visualize the tree on iTOL
- **prophage_regions.tsv** : Location of the prophage regions in al the samples
- **Panaroo folder**
- output from running [panaroo](https://github.com/gtonkinhill/panaroo)
Raw data
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