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

haplotigs

meta:map

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

]

*.hap.fa:file

Fasta file containing purged haplotigs

*.hap.fa

purged

meta:map

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

]

*.purged.fa:file

Fasta file purged of duplicated haplotigs

*.purged.fa

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

github.com/dfguan/purge_dups 10.1093/bioinformatics/btaa025
Github user mahesh-panchal
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