# Bakta

## Installation

conda create -n bakta
conda activate bakta
conda install -c conda-forge -c bioconda bakta

## Database download
Bakta requires a mandatory database which is publicly hosted at Zenodo: DOI We provide 2 types: full and light. To get best annotation results and to use all features, we recommend using the full (default). If you seek for maximum runtime performance or if download time/storage requirements are an issue, please try the light version. Further information is provided in the database section below.

List available DB versions (available as either full or light):

`bakta_db list`

To download the most recent compatible database version we recommend to use the internal database download & setup tool:

`bakta_db download --output <output-path> --type [light|full]`

Of course, the database can also be downloaded and installed manually:

`wget https://zenodo.org/record/14916843/files/db-light.tar.xz`

`bakta_db install -i db-light.tar.xz`

If required, or desired, the AMRFinderPlus DB can also be updated manually:

`amrfinder_update --force_update --database db-light/amrfinderplus-db/`

## Analysis

### Genome annotation

bakta --db ./bakta/db/ --output bakta --verbose --threads 20

### Genome annotation for multiple genomes

#### Script

#!/bin/bash

outputdir="bakta"
fnadir="/path/to/fna/files/fna_coded"
extension=".fna"
cpus=4
dbdir="/path/to/bakta/db"

# Create output directory if it doesn't exist
if [ ! -d "$outputdir" ]; then
    mkdir "$outputdir"
fi

allfna=("${fnadir}"/*"${extension}")

for file in "${allfna[@]}"
do
    bname=$(basename "$file" "${extension}")

    bakta --db "$dbdir" --prefix "$bname" --output "$outputdir/$bname" --verbose "$file"

done