recipe fqtrim

fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing machines.

Homepage:

https://ccb.jhu.edu/software/fqtrim/

License:

Artistic License 2.0

Recipe:

/fqtrim/meta.yaml

package fqtrim

(downloads) docker_fqtrim

versions:

0.9.7-7,  0.9.7-6,  0.9.7-5,  0.9.7-4,  0.9.7-3,  0.9.7-2,  0.9.7-1,  0.9.7-0

depends gclib:

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends zlib:

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 fqtrim

and update with::

   mamba update fqtrim

To create a new environment, run:

mamba create --name myenvname fqtrim

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/fqtrim:<tag>

(see `fqtrim/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/fqtrim/README.html)