Description

Induce a variation graph in GFA format from alignments in PAF format

Input

Name (Type)
Description
Pattern

meta (map)

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

]

paf (list)

comma-separated PAF file(s) of alignments, single entry allowed

[*.{paf,paf.gz},*.{paf,paf.gz},...]

fasta (file)

FASTA file used to generate alignments

*.{fa,fa.gz,fasta,fasta.gz}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

gfa (file)

Variation graph in GFA 1.0 format

*.{gfa}

versions (file)

File containing software versions

versions.yml
included in
pangenome
author
Github user heuermh
get in touch
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Tools

seqwish
MIT

seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences and their alignments.

github.com/ekg/seqwish