Description

Metagenome binning of contigs

Input

name:type
description
pattern

meta:map

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

]

fasta:file

Fasta file of the assembled contigs

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

depth:file

Optional text file listing the coverage per contig pre-generated by metabat2_jgisummarizebamcontigdepths

*.txt

Output

name:type
description
pattern

tooshort

meta:map

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

]

*.tooShort.fa.gz:file

Contigs that did not pass length filtering

*.tooShort.fa.gz

lowdepth

meta:map

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

]

*.lowDepth.fa.gz:file

Contigs that did not have sufficient depth for binning

*.lowDepth.fa.gz

unbinned

meta:map

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

]

*.unbinned.fa.gz:file

Contigs that pass length and depth filtering but could not be binned

*.unbinned.fa.gz

membership

meta:map

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

]

*.tsv.gz:file

cluster memberships as a matrix format.

*.tsv.gz

fasta

meta:map

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

]

*[!lowDepth|tooShort|unbinned].fa.gz:file

Bins created from assembled contigs in fasta file

*.fa.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

metabat2
BSD-3-clause-LBNL

Metagenome binning