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

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

2.2.0-2, 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 >=7.3.0

• libstdcxx-ng >=7.3.0

• perl

• python >=3.6,<3.7.0a0

• python_abi 3.6.* *_cp36m

Required By

• piret

• funannotate

• bismark

Installation

With an activated Bioconda channel (see 2. 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/.

Link to this page

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