Description

Annotation of bacterial genomes (isolates, MAGs) and plasmids

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

fasta (file)

FASTA file to be annotated. Has to contain at least a non-empty string dummy value.

db (file)

Path to the Bakta database. 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)

prodigal_tf (file)

Training file to use for Prodigal (optional)

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

txt (file)

genome statistics and annotation summary

*.txt

tsv (file)

annotations as simple human readble tab separated values

*.tsv

gff (file)

annotations & sequences in GFF3 format

*.gff3

gbff (file)

annotations & sequences in (multi) GenBank format

*.gbff

embl (file)

annotations & sequences in (multi) EMBL format

*.embl

fna (file)

replicon/contig DNA sequences as FASTA

*.fna

faa (file)

CDS/sORF amino acid sequences as FASTA

*.faa

ffn (file)

feature nucleotide sequences as FASTA

*.ffn

hypotheticals_tsv (file)

additional information on hypothetical protein CDS as simple human readble tab separated values

*.hypotheticals.tsv

hypotheticals_faa (file)

hypothetical protein CDS amino acid sequences as FASTA

*.hypotheticals.faa
included in
funcscan pathogensurveillance
authors
Github user rpetit3 Github user oschwengers Github user jfy133
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

bakta
GPL v3

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

github.com/oschwengers/bakta 10.1099/mgen.0.000685