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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

bed (file)

A bed file of sequences purged of false duplications

*.bed

log (file)

A log of the tool output

*.log
author
Github user mahesh-panchal
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Tools

purgedups
MIT

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

github.com/dfguan/purge_dups 10.1093/bioinformatics/btaa025