recipe polyat

Command-line tool to quantify poly-A/T homopolymers within FASTQ sequencing reads.

Homepage:

https://github.com/DaanJansen94/polyat

Documentation:

https://github.com/DaanJansen94/polyat/blob/master/README.md

License:

GPL / GPL-3.0-only

Recipe:

/polyat/meta.yaml

polyat counts poly-A/T homopolymers across FASTQ reads (>=10/15/20 nt), summarizes per sample, and writes both TSV and HTML reports with interactive filters.

package polyat

(downloads) docker_polyat

versions:

0.1.2-0

depends python:

>=3.8

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 polyat

and update with::

   mamba update polyat

To create a new environment, run:

mamba create --name myenvname polyat

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/polyat:<tag>

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