Description

Purge haplotigs and overlaps for an assembly

Input

name:type
description
pattern

meta:map

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

]

basecov:file

A file containing a histogram of base coverage. Obtained from PURGEDUPS_PBCSTAT

*.PB.base.cov

cutoff:file

A file containing duplication cutoff points. Obtained from PURGEDUPS_CALCUTS

*.cutoffs

paf:file

A file of assembly alignments to itself

*.paf(.gz)?

Output

name:type
description
pattern

bed

meta:map

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

]

*.dups.bed:file

A bed file of sequences purged of false duplications

*.bed

log

meta:map

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

]

*.purge_dups.log:file

A log of the tool output

*.log

versions

versions.yml:file

File containing software versions

versions.yml

Tools

purgedups
MIT

Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth