recipe quasirecomb

Software of Inference of Quasispecies subjected to Recombination

Homepage:

https://github.com/cbg-ethz/QuasiRecomb

License:

GPL3 / GNU GPLv3

Recipe:

/quasirecomb/meta.yaml

Links:

biotools: QuasiRecomb, doi: 10.1089/cmb.2012.0232

QuasiRecomb presents a jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. It offers an implementation of the EM algorithm to find maximum a posteriori estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies.

package quasirecomb

versions:

1.2-1,  1.2-0

depends openjdk:

>=8

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 quasirecomb

and update with::

   mamba update quasirecomb

To create a new environment, run:

mamba create --name myenvname quasirecomb

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/quasirecomb:<tag>

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

Notes

QuasiRecomb is a Java program that comes with a custom wrapper shell script.

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