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

(downloads) docker_hisat2

versions:
2.2.1-8,  2.2.1-7,  2.2.1-6,  2.2.1-5,  2.2.1-4,  2.2.1-3,  2.2.1-2,  2.2.1-0,  2.2.0-4, 

2.2.1-8,  2.2.1-7,  2.2.1-6,  2.2.1-5,  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:

>=13

depends libstdcxx:

>=13

depends perl:

depends python:

>3.5

requirements:

additional platforms:
linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install hisat2

and update with::

   mamba update hisat2

To create a new environment, run:

mamba create --name myenvname hisat2

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, 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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