# Bakta 1.0


## Bakta: Rapid & standardized annotation of bacterial genomes & plasmids

Bakta is a tool for the rapid & standardized annotation of bacterial genomes
& plasmids. It provides dbxref-rich and sORF-including annotations in
machine-readable JSON & bioinformatics standard file formats for automatic
downstream analysis.

Activate your environment; `qrsh` to an available node:

```console
bash
source /local/cluster/bakta/activate.sh
```

Location (of binary and database) and version:

```console
$ which bakta
/local/cluster/bakta/bin/bakta
$ bakta --version
bakta 1.0
$ echo $BAKTA_DB
/nfs1/CGRB/databases/bakta/latest
```

help message:

```console
$ bakta --help
usage: bakta [--db DB] [--min-contig-length MIN_CONTIG_LENGTH] [--prefix PREFIX] [--output OUTPUT] [--genus GENUS] [--species SPECIES] [--strain STRAIN] [--plasmid PLASMID] [--complete] [--prodigal-tf PRODIGAL_TF]
             [--translation-table {11,4}] [--gram {+,-,?}] [--locus LOCUS] [--locus-tag LOCUS_TAG] [--keep-contig-headers] [--replicons REPLICONS] [--skip-trna] [--skip-tmrna] [--skip-rrna] [--skip-ncrna]
             [--skip-ncrna-region] [--skip-crispr] [--skip-cds] [--skip-sorf] [--skip-gap] [--skip-ori] [--help] [--verbose] [--threads THREADS] [--tmp-dir TMP_DIR] [--version]
             <genome>

Rapid & standardized annotation of bacterial genomes & plasmids.

positional arguments:
  <genome>              Genome sequences in (zipped) fasta format

Input / Output:
  --db DB, -d DB        Database path (default = <bakta_path>/db). Can also be provided as BAKTA_DB environment variable.
  --min-contig-length MIN_CONTIG_LENGTH, -m MIN_CONTIG_LENGTH
                        Minimum contig size (default = 1)
  --prefix PREFIX, -p PREFIX
                        Prefix for output files
  --output OUTPUT, -o OUTPUT
                        Output directory (default = current working directory)

Organism:
  --genus GENUS         Genus name
  --species SPECIES     Species name
  --strain STRAIN       Strain name
  --plasmid PLASMID     Plasmid name

Annotation:
  --complete            All sequences are complete replicons (chromosome/plasmid[s])
  --prodigal-tf PRODIGAL_TF
                        Path to existing Prodigal training file to use for CDS prediction
  --translation-table {11,4}
                        Translation table: 11/4 (default = 11)
  --gram {+,-,?}        Gram type: +/-/? (default = '?')
  --locus LOCUS         Locus prefix (default = 'contig')
  --locus-tag LOCUS_TAG
                        Locus tag prefix (default = autogenerated)
  --keep-contig-headers
                        Keep original contig headers
  --replicons REPLICONS, -r REPLICONS
                        Replicon information table (tsv/csv)

Workflow:
  --skip-trna           Skip tRNA detection & annotation
  --skip-tmrna          Skip tmRNA detection & annotation
  --skip-rrna           Skip rRNA detection & annotation
  --skip-ncrna          Skip ncRNA detection & annotation
  --skip-ncrna-region   Skip ncRNA region detection & annotation
  --skip-crispr         Skip CRISPR array detection & annotation
  --skip-cds            Skip CDS detection & annotation
  --skip-sorf           Skip sORF detection & annotation
  --skip-gap            Skip gap detection & annotation
  --skip-ori            Skip oriC/oriT detection & annotation

General:
  --help, -h            Show this help message and exit
  --verbose, -v         Print verbose information
  --threads THREADS, -t THREADS
                        Number of threads to use (default = number of available CPUs)
  --tmp-dir TMP_DIR     Location for temporary files (default = system dependent auto detection)
  --version             show program's version number and exit

Citation:
Schwengers O., Goesmann A. (2021)
Bakta: comprehensive and rapid annotation of bacterial genomes.
GitHub https://github.com/oschwengers/bakta
```

### FAQ

* __AMRFinder fails__ If AMRFinder constantly crashes even on fresh setups and
  Bakta's database was downloaded manually, then AMRFinder needs to setup its
  own internal database. This is required only once: `amrfinder_update
  --force_update --database <bakta-db>/amrfinderplus-db`. You could also try
  Bakta's internal database download logic automatically taking care of this:
  `bakta_db download --output <bakta-db>`
* __Nice, but I'm mising XYZ...__ Bakta is quite new and we're keen to constantly
  improve it and further expand its feature set. In case there's anything
  missing, please do not hesitate to open an issue and ask for it!
* __Bakta is running too long without CPU load... why?__ Bakta takes advantage
  of an SQLite DB which results in high storage IO loads. If this DB is stored
  on a remote / network volume, the lookup of IPS/PSC annotations might take a
  long time. In these cases, please, consider moving the DB to a local volume
  or hard drive.

software ref: <https://github.com/oschwengers/bakta>  
research ref: <https://github.com/oschwengers/bakta#citation>