Description

ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

reads{:bash}

:file

List of input paired-end FastQ files (R1 and R2). Must be paired-end reads; ABySS requires paired reads for assembly.

*.{fastq.gz,fastq,fq.gz,fq}

merged{:bash}

:file

Optional merged/overlapping paired-end reads or supplementary single-end reads. Use empty list [] if not available.

*.{fastq.gz,fastq,fq.gz,fq}

kmersize{:bash}

:integer

K-mer size for assembly. Must be an odd number.

Output

name:type
description
pattern

contigs{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*-contigs.fa.gz{:bash}

:file

Assembled contigs in FASTA format

*-contigs.fa.gz

scaffolds{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*-scaffolds.fa.gz{:bash}

:file

Assembled scaffolds in FASTA format

*-scaffolds.fa.gz

stats{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*-stats{:bash}

:file

Assembly statistics file

*-stats

log{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*-abyss.log{:bash}

:file

ABySS assembly log file

*-abyss.log

versions_abyss{:bash}

${task.process}{:bash}

:string

The name of the process

abyss{:bash}

:string

The name of the tool

abyss-pe version | grep abyss | cut -d" " -f3{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

abyss{:bash}

:string

The name of the tool

abyss-pe version | grep abyss | cut -d" " -f3{:bash}

:eval

The expression to obtain the version of the tool

Tools

abyss
GPL v3

Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler.

github.com/bcgsc/abyss/blob/v2.3.10/README.md https://github.com/bcgsc/abyss 10.1101/gr.214346.116
maintainer
Github user LiaOb21
get in touch
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