recipe telogator2

Analyze allele-specific telomere length from PacBio and Nanopore reads

Homepage:

https://github.com/zstephens/telogator2

Documentation:

https://github.com/zstephens/telogator2/blob/main/README.md

License:

MIT / MIT

Recipe:

/telogator2/meta.yaml

Telogator2 is a bioinformatics tool for analyzing telomeres from long-read sequencing data. It measures allele-specific telomere length and characterizes telomere variant repeat (TVR) sequences from PacBio HiFi and Oxford Nanopore sequencing platforms. The tool supports human and non-human reference genomes and provides detailed output including TSV results and visualization plots.

package telogator2

(downloads) docker_telogator2

versions:

2.2.2-0

depends biopython:

>=1.86

depends matplotlib-base:

>=3.3.4

depends minimap2:

depends numpy:

>=1.19.0

depends pysam:

>=0.16.0,<=0.22.0

depends python:

>=3.10

depends pywavelets:

>=1.1.1

depends scipy:

>=1.6.0

requirements:

additional platforms:
linux-aarch64,  osx-arm64

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 telogator2

and update with::

   mamba update telogator2

To create a new environment, run:

mamba create --name myenvname telogator2

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/telogator2:<tag>

(see `telogator2/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/telogator2/README.html)