recipe eukbin

BUSCO-guided binning for eukaryotic metagenomes

Homepage:

https://github.com/weiwei12456/eukbin

Documentation:

https://github.com/weiwei12456/eukbin/blob/main/README.md

License:

MIT / MIT

Recipe:

/eukbin/meta.yaml

EukBin is a specialized binning tool for eukaryotic metagenomes that combines repeat-masked tetranucleotide frequency (TNF), multi-sample coverage information, BUSCO marker gene constraints, and deep learning (β-VAE with contrastive loss) with ploidy-aware refinement.

Key features: - Repeat-masked TNF features to handle repeat-rich eukaryotic genomes - BUSCO-guided constraints for accurate bin estimation - Ploidy-aware refinement (haplotig detection for diploid/polyploid genomes) - Deep learning with β-VAE and contrastive loss - Supports multi-sample binning

This package includes: - eukbin run: Complete binning pipeline (M1-M6 modules) - eukbin evaluate: Quality assessment for any binning tool - eukbin report: Multi-tool comparison report

package eukbin

(downloads) docker_eukbin

versions:

0.1.0-0

depends biopython:

>=1.78

depends numpy:

>=1.19

depends pandas:

>=1.0

depends python:

>=3.14,<3.15.0a0

depends pytorch:

>=1.9

depends pyyaml:

depends scikit-learn:

>=0.24

depends scipy:

>=1.5

depends tqdm:

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 eukbin

and update with::

   mamba update eukbin

To create a new environment, run:

mamba create --name myenvname eukbin

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/eukbin:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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