recipe snpick

A fast and memory-efficient tool for SNP extraction from genomic alignments.

Homepage:

https://github.com/PathoGenOmics-Lab/snpick

License:

GPL3 / GPL-3.0-or-later

Recipe:

/snpick/meta.yaml

snpick is a Rust-based tool designed for extracting SNPs efficiently from large genomic alignments, with minimal RAM usage and high performance. It outputs variable sites in alignment files and provides VCF generation.

package snpick

versions:

1.0.0-0

depends bzip2:

>=1.0.8,<2.0a0

depends libzlib:

>=1.2.13,<2.0a0

depends openssl:

>=3.4.0,<4.0a0

depends xz:

>=5.2.6,<6.0a0

depends zlib:

>=1.2.13,<2.0a0

requirements:

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 snpick

and update with::

   mamba update snpick

To create a new environment, run:

mamba create --name myenvname snpick

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/snpick:<tag>

(see `snpick/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an badge with the following MarkDown:

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