recipe notramp

Super-fast Normalization and Trimming for Amplicon Sequencing Data (Long- and Short-read)

Homepage:

https://github.com/simakro/NoTrAmp.git

Documentation:

https://github.com/simakro/NoTrAmp/blob/main/README.md

License:

BSD / BSD-2

Recipe:

/notramp/meta.yaml

NoTrAmp is a Tool for super fast trimming and read-depth normalization of amplicon reads. It is designed to be used in amplicon-tiling panels (or similar multiplexed amplicon sequencing approaches) to cap coverage of each amplicon (if desired) and to trim amplicons to their appropriate length removing barcodes, adpaters and primers (if desired) in a single clipping step.

NoTrAmp is suitable for use with both long (e.g. ONT/PacBio) and short reads (e.g Illumina). When using reads that are significantly shorter than amplicon sizes, you should adjust the minimum required alignment length using the --set_min_len argument.

See the projects [home](https://github.com/simakro/NoTrAmp) for usage and additional documentation.

package notramp

(downloads) docker_notramp

versions:

1.1.7-0,  1.1.6-1,  1.1.6-0,  1.0.5-0

depends minimap2:

depends psutil:

depends python:

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 notramp

and update with::

   mamba update notramp

To create a new environment, run:

mamba create --name myenvname notramp

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/notramp:<tag>

(see `notramp/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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