recipe hisat-3n

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

Homepage:

https://github.com/fulcrumgenomics/hisat-3n

License:

GPL / GPL-3.0

Recipe:

/hisat-3n/meta.yaml

Links:

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

HISAT-3N (hierarchical indexing for spliced alignment of transcripts - 3 nucleotides) is designed for nucleotide conversion sequencing technologies and implemented based on HISAT2.

package hisat-3n

(downloads) docker_hisat-3n

versions:

0.0.3-0

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 hisat-3n

and update with::

   mamba update hisat-3n

To create a new environment, run:

mamba create --name myenvname hisat-3n

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/hisat-3n:<tag>

(see `hisat-3n/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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