Description

Generate the input coverage table for CONCOCT using a BEDFile

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bed (file)

BED file describing where each contig was cut up (typically output from CONCOCT’s cut_up_fasta.py)

*.bed

bamfiles (file)

A single or list of BAM files of reads mapped back to original contigs (prior cutting up)

*.bam

baifiles (file)

A single or list of BAM index files (.bai) corresponding to BAM

*.bam

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

tsv (file)

Contig coverage table

*.tsv
included in
mag
author
Github user jfy133
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Tools

concoct
FreeBSD

Clustering cONtigs with COverage and ComposiTion

concoct.readthedocs.io/en/latest https://github.com/BinPro/CONCOCT 10.1038/nmeth.3103