recipe hisat2

Graph-based alignment of next generation sequencing reads to a population of genomes.

Homepage:

http://daehwankimlab.github.io/hisat2

Documentation:

https://daehwankimlab.github.io/hisat2/manual/

Developer docs:

https://github.com/DaehwanKimLab/hisat2

License:

GPL / GPL-3.0

Recipe:

/hisat2/meta.yaml

Links:

biotools: HISAT2, doi: 10.1038/nmeth.3317, doi: 10.1038/s41587-019-0201-4, usegalaxy-eu: hisat2

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.

package hisat2

Versions:

2.2.1-4,  2.2.1-3,  2.2.1-2,  2.2.1-0,  2.2.0-4,  2.2.0-3,  2.2.0-2,  2.2.0-1,  2.2.0-0, 

2.2.1-4,  2.2.1-3,  2.2.1-2,  2.2.1-0,  2.2.0-4,  2.2.0-3,  2.2.0-2,  2.2.0-1,  2.2.0-0,  2.1.0-4,  2.1.0-3,  2.1.0-2,  2.1.0-1,  2.1.0-0,  2.0.5-2,  2.0.5-1,  2.0.4-1,  2.0.4-0,  2.0.3beta-0,  2.0.2beta-0,  2.0.1beta-0,  2.0.0beta-0

Depends:

• libgcc-ng >=10.3.0

• libstdcxx-ng >=10.3.0

• perl

• python >3.5

Required By:

• funannotate

• piret

• smartmap

• hocort

• bismark

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install hisat2

and update with:

conda update hisat2

or use the docker container:

docker pull quay.io/biocontainers/hisat2:<tag>

(see hisat2/tags for valid values for <tag>)

Notes

Pre-built indices for HISAT2 can be downloaded from https://daehwankimlab.github.io/hisat2/download/.

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