Annotation of bacterial genomes (isolates, MAGs) and plasmids
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
:file
FASTA file to be annotated. Has to contain at least a non-empty string dummy value.
*.{fa,fas,fna,fasta}
db{:bash}
:file
Path to the Bakta database directory. Must have amrfinderplus database directory already installed within it (in a directory called ‘amrfinderplus-db/’).
proteins{:bash}
:file
FASTA/GenBank file of trusted proteins to first annotate from (optional)
*.{fa,fas,fna,fasta,faa}
prodigal_tf{:bash}
:file
Training file to use for Prodigal for CDS prediction(optional)
*.{tf,trn}
regions{:bash}
:file
GFF3 or GenBank file of pre-annotated regions (optional)
*.{gbff,gff3}
hmms{:bash}
:file
HMM database file for custom annotation (optional)
*.hmm
Output
name:type
description
pattern
embl{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.embl{:bash}
:file
annotations & sequences in (multi) EMBL format
*.embl
faa{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.faa{:bash}
:file
CDS/sORF amino acid sequences as FASTA
*.faa
ffn{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.ffn{:bash}
:file
feature nucleotide sequences as FASTA
*.ffn
fna{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.fna{:bash}
:file
replicon/contig DNA sequences as FASTA
*.fna
gbff{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.gbff{:bash}
:file
annotations & sequences in (multi) GenBank format
*.gbff
gff{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.gff3{:bash}
:file
annotations & sequences in GFF3 format
*.gff3
hypotheticals_tsv{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.hypotheticals.tsv{:bash}
:file
additional information on hypothetical protein CDS as simple human readable tab separated values
*.hypotheticals.tsv
hypotheticals_faa{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.hypotheticals.faa{:bash}
:file
hypothetical protein CDS amino acid sequences as FASTA
*.hypotheticals.faa
tsv{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.tsv{:bash}
:file
annotations as simple human readable tab separated values
*.tsv
txt{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.txt{:bash}
:file
genome statistics and annotation summary
*.txt
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
bakta
GPL v3
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
