Description

Builds HISAT2 index for reference genome

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fasta (file)

Reference fasta file

*.{fa,fasta,fna}

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

gtf (file)

Reference gtf annotation file

*.{gtf}

meta3 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

splicesites (file)

Splices sites in gtf file

*.{txt}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

index (file)

HISAT2 genome index file

*.ht2

versions (file)

File containing software versions

versions.yml
included in
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maintainer
Github user ntoda03
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Tools

hisat2
MIT

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.

daehwankimlab.github.io/hisat2 daehwankimlab.github.io/hisat2/manual 10.1038/s41587-019-0201-4