Description

Assembles bacterial genomes

Input

name:type
description
pattern

meta:map

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

]

shortreads:file

List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

longreads:file

List of input FastQ files of size 1, PacBio or Nanopore long reads.

Output

name:type
description
pattern

scaffolds

meta:map

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

]

*.scaffolds.fa.gz:file

Fasta file containing scaffolds

*.{scaffolds.fa.gz}

gfa

meta:map

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

]

*.assembly.gfa.gz:file

gfa file containing assembly

*.{assembly.gfa.gz}

log

meta:map

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

]

*.log:file

unicycler log file

*.{log}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

unicycler
GPL v3

Hybrid assembly pipeline for bacterial genomes