- 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:
2.2.2-0,2.2.1-8,2.2.1-7,2.2.1-6,2.2.1-5,2.2.1-4,2.2.1-3,2.2.1-2,2.2.1-0,2.2.2-0,2.2.1-8,2.2.1-7,2.2.1-6,2.2.1-5,2.2.1-4,2.2.1-3,2.2.1-2,2.2.1-0,2.2.0-4,2.2.0-3,2.2.0-2,2.2.0-1,2.2.0-0,2.1.0-4,2.1.0-3,2.1.0-2,2.1.0-1,2.1.0-0,2.0.5-2,2.0.5-1,2.0.4-1,2.0.4-0,2.0.3beta-0,2.0.2beta-0,2.0.1beta-0,2.0.0beta-0- Depends:
on libgcc
>=13on libstdcxx
>=13on perl
on python
>3.5
- Additional platforms:
linux-aarch64,osx-arm64
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install hisat2
to add into an existing workspace instead, run:
pixi add hisat2
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install hisat2
Alternatively, to install into a new environment, run:
conda create -n envname hisat2
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/hisat2:<tag>
(see hisat2/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Notes¶
Pre-built indices for HISAT2 can be downloaded from https://daehwankimlab.github.io/hisat2/download/.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/hisat2/README.html)
