Description

Separates out sequences purged of falsely duplicated sequences.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

assembly (file)

Draft assembly in fasta format

*.fasta

bed (file)

Bed file listing duplicated sequences, produced by PURGEDUPS_PURGEDUPS

*.bed

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

haplotigs (file)

Fasta file containing purged haplotigs

*.hap.fa

purged (file)

Fasta file purged of duplicated haplotigs

*.purged.fa
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