Description

contiguate draft genome assembly

Input

name:type
description
pattern

meta:map

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

]

scaffold:file

Fasta file containing scaffold

*.{fasta,fa}

fasta:file

FASTA reference file

*.{fasta,fa}

Output

name:type
description
pattern

results

meta:map

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

]

*.abacas*:file

List containing abacas output files [ ‘test.abacas.bin’, ‘test.abacas.fasta’, ‘test.abacas.gaps’, ‘test.abacas.gaps.tab’, ‘test.abacas.nucmer.delta’, ‘test.abacas.nucmer.filtered.delta’, ‘test.abacas.nucmer.tiling’, ‘test.abacas.tab’, ‘test.abacas.unused.contigs.out’, ‘test.abacas.MULTIFASTA.fa’ ]

*.{abacas}*

versions

versions.yml:file

File containing software versions

versions.yml

Tools

abacas
GPL v2-or-later

ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence.