Description

A very fast OLC-based de novo assembler for noisy long reads

Input

name:type
description
pattern

meta:map

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

reads:file

List of input PacBio/ONT FastQ files.

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

paf:file

Alignment in PAF format

*{.paf,.paf.gz}

Output

name:type
description
pattern

gfa

meta:map

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

*.gfa.gz:file

Assembly graph

*.gfa.gz

assembly

meta:map

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

*.fasta.gz:file

Genome assembly

*.fasta.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

miniasm
MIT

Ultrafast de novo assembly for long noisy reads (though having no consensus step)