Description

Create a GEM index from a FASTA file

Input

name:type
description
pattern

meta:map

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

]

fasta:file

A reference FASTA file to index

*.{fasta,fa,fna}

Output

name:type
description
pattern

index

meta:map

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

]

*.gem:file

The GEM index file

*.gem

log

meta:map

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

]

*.log:file

The execution log

*.log

versions

versions.yml:file

File containing software versions

versions.yml

Tools

gem2
Custom

GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability.