Package Recipe 'binspreader'

recipe binspreader

BinSPreader is a tool for improving existing binning using assembly graph and other sources of connectivity information

Homepage:: https://cab.spbu.ru/software/binspreader/
License:: GPL2 / GPL-2.0-only
Recipe:: /binspreader/meta.yaml
Links:: biotools: binspreader, doi: 10.1016/j.isci.2022.104770

BinSPreader is a novel tool that attempts to refine metagenome-assembled genomes (MAGs) obtained from existing tools. BinSPreader exploits the assembly graph topology and other connectivity information, such as paired-end and Hi-C reads, to refine the existing binning, correct binning errors, propagate binning from longer contigs to shorter contigs and infer contigs belonging to multiple bins.

package binspreader¶

Versions:

3.16.0.dev-0

Depends:

on __glibc >=2.17,<3.0.a0
on bzip2 >=1.0.8,<2.0a0
on libgcc-ng >=12
on libstdcxx-ng >=12
on libzlib >=1.2.13,<1.3.0a0
on openmp
on sysroot_linux-64 >=2.17

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 binspreader

to add into an existing workspace instead, run:

pixi add binspreader

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 binspreader

Alternatively, to install into a new environment, run:

conda create -n envname binspreader

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/binspreader:<tag>

(see binspreader/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/binspreader/README.html)