recipe btrim

This tool is made to remove "tips" (short dead ends) from a compacted de Bruijn graph and more generally to remove sequencing errors. Used in Bcool a short read corrector (https://arxiv.org/abs/1711.03336)

Homepage:

https://github.com/Malfoy/BTRIM

License:

AGPL-3.0

Recipe:

/btrim/meta.yaml

package btrim

(downloads) docker_btrim

versions:

1.0.1-6,  1.0.1-5,  1.0.1-4,  1.0.1-3,  1.0.1-2,  1.0.1-1,  1.0.0-0

depends _openmp_mutex:

>=4.5

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

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 btrim

and update with::

   mamba update btrim

To create a new environment, run:

mamba create --name myenvname btrim

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/btrim:<tag>

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

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Link to this page

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

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