- recipe hisat2
Graph-based alignment of next generation sequencing reads to a population of genomes.
- Homepage:
- Documentation:
- Developer docs:
- License:
GPL / GPL-3.0
- Recipe:
- 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:
2.2.1-7
,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
,2.2.1-7
,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:
>=12
- depends libstdcxx:
>=12
- 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/.
Download stats¶
Link to this page¶
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