Description

Performs assembly scaffolding using YaHS

Input

name:type
description
pattern

meta:map

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

hic_map:file

BED file containing coordinates of read alignments

*.{bed,bam,bin}

fasta:file

FASTA reference file

*.{fasta,fa}

fai:file

index of the reference file

*.{fai}

Output

name:type
description
pattern

scaffolds_fasta

meta:map

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

*scaffolds_final.fa:file

FASTA file with resulting contigs

*scaffolds_final.fa

scaffolds_agp

meta:map

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

*scaffolds_final.agp:file

AGP file containing contigs placing coordinates

*scaffolds_final.agp

binary

meta:map

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

*bin:file

BIN file with alignment results of Hi-C reads to the contigs in internal YaHS binary format

*bin

versions

versions.yml:file

File containing software versions

versions.yml

Tools

yahs
MIT

YaHS, yet another Hi-C scaffolding tool.