Description

Annotation of bacterial genomes (isolates, MAGs) and plasmids

Input

Name
Description
Pattern

0 ()

1 ()

db (file)

Path to the Bakta database directory. Must have amrfinderplus database directory already installed within it (in a directory called 'amrfinderplus-db/').

proteins (file)

FASTA/GenBank file of trusted proteins to first annotate from (optional)

*.{fa,fas,fna,fasta,faa}

prodigal_tf (file)

Training file to use for Prodigal for CDS prediction(optional)

*.{tf,trn}

regions (file)

GFF3 or GenBank file of pre-annotated regions (optional)

*.{gbff,gff3}

hmms (file)

HMM database file for custom annotation (optional)

*.hmm

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

bakta Documentation

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.

doi: 10.1099/mgen.0.000685License: GPL v3
Authors