SemiBin: Metagenomic Binning Using Siamese Neural Networks for short and long reads

A dedicated semibin page with documentation is available at https://semibin.rtfd.io. This page is just a summary.

SemiBin is a tool for metagenomic binning with deep learning, handles both short and long reads.

If you use this software in a publication please cite:

Pan, S., Zhu, C., Zhao, XM. et al. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments. Nat Commun 13, 2326 (2022). https://doi.org/10.1038/s41467-022-29843-y

The self-supervised approach and the algorithms used for long-read datasets (as well as their benchmarking) are described in

Pan, S.; Zhao, XM; Coelho, LP. SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing in Bioinformatics https://doi.org/10.1093/bioinformatics/btad209