recipe samstats

SAM file alignment statistics at the read level

Homepage:

https://github.com/kundajelab/SAMstats

License:

MIT

Recipe:

/samstats/meta.yaml

Scripts that implement samtools flagstat functionality, but provide statistics for individual reads rather than individual alignments

package samstats

(downloads) docker_samstats

versions:

0.2.2-0,  0.2.1-0

depends multiprocess:

depends python:

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 samstats

and update with::

   mamba update samstats

To create a new environment, run:

mamba create --name myenvname samstats

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/samstats:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/samstats/README.html)