- recipe metaprob
assembly-assisted tool for un-supervised metagenomic binning
- Homepage:
- License:
copyright
- Recipe:
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¶
- Versions:
2-1,2-0- Depends:
on boost
1.61*on eigen
on libgcc
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install metaprob
to add into an existing workspace instead, run:
pixi add metaprob
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install metaprob
Alternatively, to install into a new environment, run:
conda create -n envname metaprob
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/metaprob:<tag>
(see metaprob/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/metaprob/README.html)
