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](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. [](https://anaconda.org/bioconda/semibin) [](https://github.com/BigDataBiology/SemiBin/actions/workflows/semibin_test.yml) [](https://semibin.readthedocs.io/en/latest/?badge=latest) [](https://opensource.org/licenses/MIT) 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](https://doi.org/10.1038/s41467-022-29843-y). *Nat Commun* **13,** 2326 (2022). [https://doi.org/10.1038/s41467-022-29843-y](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](https://doi.org/10.1101/2023.01.09.523201). *bioRxiv preprint* 2023.01.09.523201; [https://doi.org/10.1101/2023.01.09.523201](https://doi.org/10.1101/2023.01.09.523201)