Description

Taxonomic classification of long DNA sequences and metagenome assembled genomes (e.g. MAGs / bins).

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

bins{:bash}

:file

One or more nucleotide FASTA file containing binned long DNA sequences.

*.{fasta,fna,fa,fas}

meta2{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

database{:bash}

:directory

Directory containing CAT_pack database files (e.g. output from CAT_pack prepare)

*/

meta3{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

taxonomy{:bash}

:directory

Directory containing CAT_pack taxonomy files (e.g. output from CAT_pack prepare)

*/

meta4{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

proteins{:bash}

:directory

Optional pre predicted-made proteins FASTA

*.{fasta,faa,fa,fas}

meta5{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

diamond_table{:bash}

:directory

Optional pre-made DIAMOND alignment table

*

bin_suffix{:bash}

:string

Suffix to search for in the input files when bins is a directory.

Output

name:type
description
pattern

orf2lca{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.ORF2LCA.txt{:bash}

:file

A TSV file with per-ORF hit stats and identified lineage

*.ORF2LCA.txt

bin2classification{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.bin2classification.txt{:bash}

:file

A TSV file with per-bin hit stats and assignment justification information

*.bin2classification.txt

log{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.log{:bash}

:file

Log file with run messages and basic statistics

diamond{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.diamond{:bash}

:file

Intermediate DIAMOND TSV summary output file with alignment results

faa{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.predicted_proteins.faa{:bash}

:file

FAA file of DIAMOND predicted proteins hits

gff{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.gff{:bash}

:file

GFF file of DIAMOND predicted proteins hits

versions_catpack{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

catpack{:bash}

:string

The tool name

CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

catpack{:bash}

:string

The name of the tool

CAT_pack --version | sed 's/CAT_pack pack v//g;s/ .*//g'{:bash}

:eval

The expression to obtain the version of the tool

Tools

catpack
MIT

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

github.com/MGXlab/CAT_pack 10.1186/s13059-019-1817-x
included in
magseqsubmit
maintainer
Github user jfy133
get in touch
Ask a question on Slack Open an issue on GitHub