Adam Gudyś

Vclust (the ultra-fast, high-accuracy tool for viral genome comparison & clustering) is now published: nature.com/articles/s4159… Great collaboration with @a_zielezinski, @AdamGudys, UAM guys, and Bas E.Dutilh

I am happy to announce that ProteStAr, our compressor of CIF/PDB files with 3D atom coordinates, is now published at Bioinformatics. With this, you can store the whole ESM Atlas or AlphaFold DB in a few files (rather than 200M+) with fast random access. doi.org/10.1093/bioinf…

Excited to share Vclust! It's a fast and accurate tool for calculating intergenomic similarities (like ANI) and clustering virus/#phage genomes/contigs according to ICTV and MIUViG standards. 💻 Tool: github.com/refresh-bio/vc… 📄 Preprint: biorxiv.org/content/10.110… Thread! 1/6 ↓

After a few years of development, Kmer-db v.2, our tool for finding similar sequences in large collections of genomic data (even millions of viral genomes), is ready. If interested, take a look at the GitHub repo and related paper. github.com/refresh-bio/km… biorxiv.org/content/10.110…

Clustering large datasets can be challenging. Fortunately, even slow methods can sprint for sparse similarity matrices. Clusty offers s-, c-link, uclust, set-cover, cd-hit, leiden. The paper shows an application for 15M+ sequences. github.com/refresh-bio/cl… biorxiv.org/content/10.110…

Thinking of aligning a million of sequences? Take a look at our @COSB_CRSB review on ultra-scale protein sequence alignments. @SantusLuisa @edgano90 @sdeorowicz and @cnotred - great pleasure to work with you! authors.elsevier.com/a/1grRh,LqArQC…

NOMAD2 is an unsupervised, reference-free, ultra-fast next generation of NOMAD, revealing new insights into cancer transcriptomes. Joint work with @salzmanlab. Many thanks to all for great collab! biorxiv.org/content/10.110…