recipe lassensus

Tool for creating Lassa virus consensus sequences

Homepage:

https://github.com/DaanJansen94/lassensus

Documentation:

https://github.com/DaanJansen94/lassensus/blob/main/README.md

License:

GPL / GPL-3.0

Recipe:

/lassensus/meta.yaml

Lassensus is a command-line tool for creating consensus sequences from Lassa virus sequencing data. It provides a streamlined workflow for processing raw sequencing data into high-quality consensus sequences.

package lassensus

(downloads) docker_lassensus

versions:

0.0.3-0,  0.0.2-0

depends biopython:

>=1.80

depends ivar:

depends lassaseq:

depends medaka:

depends minimap2:

depends numpy:

>=1.20.0

depends pandas:

depends python:

>=3.11

depends requests:

>=2.25.0

depends samtools:

depends seqtk:

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 lassensus

and update with::

   mamba update lassensus

To create a new environment, run:

mamba create --name myenvname lassensus

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/lassensus:<tag>

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