recipe nxtrim

Software to remove Nextera Mate Pair adapters and categorise reads according to the orientation implied by the adapter location.

Homepage:

https://github.com/sequencing/NxTrim

License:

BSD-2-Clause

Recipe:

/nxtrim/meta.yaml

Links:

biotools: nxtrim, doi: 10.1093/bioinformatics/btv057

package nxtrim

(downloads) docker_nxtrim

versions:

0.4.3-5,  0.4.3-4,  0.4.3-3,  0.4.3-2,  0.4.3-1,  0.4.3-0

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 nxtrim

and update with::

   mamba update nxtrim

To create a new environment, run:

mamba create --name myenvname nxtrim

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/nxtrim:<tag>

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

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Link to this page

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