recipe ampligone

Ampligone is a tool which accurately removes primer sequences from FastQ NGS reads in an amplicon sequencing experiment

Homepage:

https://rivm-bioinformatics.github.io/AmpliGone/

Developer docs:

https://github.com/RIVM-bioinformatics/AmpliGone

License:

AGPL / GNU Affero General Public v3

Recipe:

/ampligone/meta.yaml

package ampligone

versions:

1.3.1-0,  1.3.0-0,  1.2.1-0,  1.2.0-0,  1.1.0-0,  1.0.3-0,  1.0.1-0

depends biopython:

>=1.79

depends mappy:

2.24

depends pandas:

>=1.3

depends parmap:

1.5.*

depends pysam:

0.19.*

depends python:

>=3.8

depends regex:

>=2021.11.10

depends rich:

12.5.*

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 ampligone

and update with::

   mamba update ampligone

To create a new environment, run:

mamba create --name myenvname ampligone

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/ampligone:<tag>

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

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