Install

SemiBin can run on Python 3.7-3.12.

Install from bioconda

Simple Mode

The simplest way to install is to use conda.

conda create -n SemiBin
conda activate SemiBin
conda install -c conda-forge -c bioconda semibin

GPU mode from conda

If you want to use SemiBin with GPU, you need to install Pytorch with GPU support.

conda create -n SemiBin
conda activate SemiBin
conda install -c conda-forge -c bioconda semibin
conda install pytorch torchvision torchaudio cudatoolkit=10.2 -c pytorch-lts

Install from source

You will need the following dependencies: - MMseqs2 - Bedtools, Hmmer - Prodigal - (optionally) Fraggenescan

You can obtain them from conda with the following commands

conda install -c conda-forge -c bioconda mmseqs2=13.45111
conda install -c bioconda bedtools hmmer fraggenescan samtools

Then, installing should be a simple matter of running:

python setup.py install

Alternative ways of running SemiBin

If you use one of these pipelines, we ask that you cite both the pipeline author and the SemiBin manuscript (as well as any other pipeline-embedded tools which contribute to your results).