usage: bakta [--db DB] [--min-contig-length MIN_CONTIG_LENGTH] [--prefix PREFIX] [--output OUTPUT] [--force]
[--genus GENUS] [--species SPECIES] [--strain STRAIN] [--plasmid PLASMID]
[--complete] [--prodigal-tf PRODIGAL_TF] [--translation-table {11,4,25}] [--gram {+,-,?}]
[--locus LOCUS] [--locus-tag LOCUS_TAG] [--locus-tag-increment {1,5,10}] [--keep-contig-headers] [--compliant]
[--replicons REPLICONS] [--regions REGIONS] [--proteins PROTEINS] [--hmms HMMS] [--meta]
[--skip-trna] [--skip-tmrna] [--skip-rrna] [--skip-ncrna] [--skip-ncrna-region]
[--skip-crispr] [--skip-cds] [--skip-pseudo] [--skip-sorf] [--skip-gap] [--skip-ori] [--skip-filter] [--skip-plot]
[--help] [--verbose] [--debug] [--threads THREADS] [--tmp-dir TMP_DIR] [--version]
<genome>
Rapid & standardized annotation of bacterial genomes, MAGs & 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/sequence size (default = 1; 200 in compliant mode)
--prefix PREFIX, -p PREFIX
Prefix for output files
--output OUTPUT, -o OUTPUT
Output directory (default = current working directory)
--force, -f Force overwriting existing output folder (except for 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 {11,4,25}
Translation table: 11/4/25 (default = 11)
--gram {+,-,?} Gram type for signal peptide predictions: +/-/? (default = ?)
--locus LOCUS Locus prefix (default = 'contig')
--locus-tag LOCUS_TAG
Locus tag prefix (default = autogenerated)
--locus-tag-increment {1,5,10}
Locus tag increment: 1/5/10 (default = 1)
--keep-contig-headers
Keep original contig/sequence headers
--compliant Force Genbank/ENA/DDJB compliance
--replicons REPLICONS, -r REPLICONS
Replicon information table (tsv/csv)
--regions REGIONS Path to pre-annotated regions in GFF3 or Genbank format (regions only, no functional annotations).
--proteins PROTEINS Fasta file of trusted protein sequences for CDS annotation
--hmms HMMS HMM file of trusted hidden markov models in HMMER format for CDS annotation
--meta Run in metagenome mode. This only affects CDS prediction.
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-pseudo Skip pseudogene detection & annotation
--skip-sorf Skip sORF detection & annotation
--skip-gap Skip gap detection & annotation
--skip-ori Skip oriC/oriT detection & annotation
--skip-filter Skip feature overlap filters
--skip-plot Skip generation of circular genome plots
General:
--help, -h Show this help message and exit
--verbose, -v Print verbose information
--debug Run Bakta in debug mode. Temp data will not be removed.
--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