recipe metaprob

assembly-assisted tool for un-supervised metagenomic binning

Homepage:

https://bitbucket.org/samu661/metaprob/

License:

copyright

Recipe:

/metaprob/meta.yaml

MetaProb is a novel assembly-assisted tool for un-supervised metagenomic binning. The novelty of MetaProb derives from solving a few important problems: how to divide reads into groups of independent reads, so that l-mer frequencies are not overestimated; how to convert l-mer counts into probabilistic sequence signatures, that will correct for variable distribution of l-mers, and for unbalanced groups of reads, in order to produce better estimates of the underlying genome statistic. We show that MetaProb is effective for both simulated and real datasets. It can accurately (with F-measures of 87 for short reads and 97 long reads) and efficiently bin short and long reads with varying abundance ratios.

package metaprob

(downloads) docker_metaprob

versions:

2-1,  2-0

depends boost:

1.61*

depends eigen:

depends libgcc:

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 metaprob

and update with::

   mamba update metaprob

To create a new environment, run:

mamba create --name myenvname metaprob

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/metaprob:<tag>

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

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Link to this page

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