@AdamGudys

computer scientist, bioinformatician, teacher, cyclist, volleyball player, dad

 Gliwice, Poland
github.com/agudys
Joined March 2022
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  • Following14
  • Followers16
Vclust (the ultra-fast, high-accuracy tool for viral genome comparison & clustering) is now published: nature.com/articles/s41592-0… Great collaboration with @a_zielezinski, @AdamGudys, UAM guys, and Bas E.Dutilh

Ultrafast and accurate sequence alignment and clustering of viral genomes

Nature Methods - Vclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.

nature.com
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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/bioinformati…

Efficient protein structure archiving using ProteStAr

AbstractMotivation. The introduction of Deep Minds’ Alpha Fold 2 enabled the prediction of protein structures at an unprecedented scale. AlphaFold Protein

academic.oup.com
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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/vclus… 📄 Preprint: biorxiv.org/content/10.1101/… Thread! 1/6 ↓
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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/kmer-… biorxiv.org/content/10.1101/…

GitHub - refresh-bio/kmer-db: Fast and memory-efficient tool for large-scale k-mer analyses...

Fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, comparison): 16 million viral contigs analyzed in less than an hour. - refresh-bio/kmer-db

github.com
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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/clust… biorxiv.org/content/10.1101/…

GitHub - refresh-bio/clusty: Clustering tool optimized for sparse distance matrices: ~16M elements...

Clustering tool optimized for sparse distance matrices: ~16M elements with ~190M connections clustered in minutes. - refresh-bio/clusty

github.com
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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…
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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/10.1101/…

NOMAD2 provides ultra-efficient, scalable, and unsupervised discovery on raw sequencing reads

NOMAD is a new, unsupervised, reference-free, and unifying algorithm that discovers regulated sequence variation through statistical analysis of k -mer composition in DNA or RNA sequencing experime...

biorxiv.org
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