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

meta (map)

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

]

results (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 (file)

File containing software versions

versions.yml
included in
viralrecon
maintainers
Github user joseespinosa
Github user drpatelh
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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.

http://abacas.sourceforge.net/documentation 10.1093/bioinformatics/btp347