recipe soapcoverage

SOAPcoverarge can calculate sequencing coverage or physical coverage as well as duplication rate and details of specific block for each segments and whole genome by using SOAP, BLAT, BLAST, BlastZ, mum- mer and MAQ aligement results with multi-thread.

Homepage:

http://soap.genomics.org.cn/soapaligner.html

License:

GPL

Recipe:

/soapcoverage/meta.yaml

package soapcoverage

(downloads) docker_soapcoverage

versions:

2.7.7-0

depends libgcc:

depends zlib:

1.2.11*

requirements:

additional platforms:

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 soapcoverage

and update with::

   mamba update soapcoverage

To create a new environment, run:

mamba create --name myenvname soapcoverage

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/soapcoverage:<tag>

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

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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/soapcoverage/README.html)