Data compression. Algorithms for genome sequencing compresion and analysis.
Gliwice, Poland
Joined August 2019
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FAMSA can now be used in a web browser:
refresh-bio.github.io/tools/…
It is compiled to WebAssembly, so all computations run locally on the device - your data never leaves your machine.
Sample timings (workstation, 16 threads) for cys family (56k seqs): 150s (default) or 20s (medoids).
Now published in Bioinformatics:
doi.org/10.1093/bioinformati…
MDCompress (biorxiv.org/content/10.64898…) is our recent proposal for storing molecular dynamics simulations. Try if you feel that your XTC files are too big or need random access features. Great collaboration with Travis Wheeler's lab.
10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, @a_zielezinski and @cnotred, for great collaboration
nature.com/articles/s41587-0…
Sebastian Deorowicz retweeted
If you have HiFi or Nanopore R10 metagenomic data, try myloasm from Jim Shaw. You will probably find more complete circular contigs to higher resolution especially for R10 or environmental samples. Scalable to >500GB data. Written in Rust. Published in
@NatureBiotech
Myloasm, our long-read metagenome assembler, is now published! w/ Max Marin & @lh3lh3
Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers for helpful feedback.
Link: rdcu.be/famFj
MDCompress (biorxiv.org/content/10.64898…) is our recent proposal for storing molecular dynamics simulations. Try if you feel that your XTC files are too big or need random access features. Great collaboration with Travis Wheeler's lab.
Sebastian Deorowicz retweeted
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/on-…. Work with @QianAlvinQin1
Sebastian Deorowicz retweeted
Longdust, a new tool to identify highly repetitive STRs, VNTRs, satellite DNA and other low-complexity regions (LCRs). Similar to SDUST but for long regions.
github.com/lh3/longdust
Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: biorxiv.org/content/10.1101/…
and GH repo: github.com/refresh-bio/FAMSA
Sebastian Deorowicz retweeted
Vclust generates fast and accurate estimation of average nucleotide identity (ANI) for viral genomes, scaling clustering to millions of genomes.
@a_zielezinski @AdamGudys @sdeorowicz @Piotr_Rozwalak @UAM_Poznan @polsl_pl @UniJena
nature.com/articles/s41592-0…
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
Recently, our SPLASH paper (nature.com/articles/s41587-0…) was published in NatBiotech. Now, we release its extended version, sc-SPLASH (biorxiv.org/content/10.1101/…), which allows reference-free analysis of single-cell data. It was a great experience to work with our collaborators on that!
Sebastian Deorowicz retweeted
The latest hifiasm can directly assemble standard @nanopore simplex R10 reads, without HERRO correction or other preprocessing, to phased contigs of contiguity comparable to HiFi assembly. Like before, you can further add ultra-long, Hi-C or trio data for better assembly.
Exciting news! The latest hifiasm release from @ChengChhy and @lh3lh3 adds beta support for @nanopore simplex R10 reads. Initial results look very promising. 🚀
Check it out: github.com/chhylp123/hifiasm…"
AGC 3.2 (assembled genome compressor) has been released. Better speed, better ratio (at least for bacteria genomes), optional low-memory decompression.
github.com/refresh-bio/agc
Sebastian Deorowicz retweeted
Happy to share our latest paper with @marekkoki on SPLASH2 for ultra-efficient reference-free discovery directly on raw sequencing reads out in @NatureBiotech, supervised by @SalzmanLab and @sdeorowicz, and with great contributions from @TBaharav.
nature.com/articles/s41587-0…
Sebastian Deorowicz retweeted
New paper online in @NatureBiotech by @sdeorowicz group and @SalzmanLab: SPLASH2 speeds up analysis of sequence variation in massive datasets.
Sebastian Deorowicz retweeted
Preprint on "BWT construction and search at the terabase scale". We can compress 100 human genomes to 11GB in 21 hours, find SMEMs with it, do affine-gap alignment and retrieve similar local haplotypes. 7.3Tb commonly sequenced bacterial genomes ⇒ 30GB arxiv.org/abs/2409.00613
Sebastian Deorowicz retweeted
Pangene now published in Bioinformatics: doi.org/10.1093/bioinformati…. In addition to showcasing applications (see the 17q21.31 inversion below), we also reviewed the theoretical formulation of bidirected graphs and discussed the definition and the finding of "bubbles" in such graphs.
ALT 17q21.31 inversion among human samples
Preprint on Exploring gene content with pangenome gene graphs: arxiv.org/abs/2402.16185. It describes pangene for building gene graphs and for calling gene-level variations which can be found at pangene.bioinweb.org.
Pleasant collaboration with @maxgmarin and @MahaFarhat.
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…
Sebastian Deorowicz retweeted
When writing bioinformatics tools, I often need unique IDs for things like temp directories. So, I created a Python package for generating fun & memorable IDs like "retired-nucleotide" or "funny-malware-7ab4" covering everything from sports to science.
github.com/aziele/unique-nam…
Sebastian Deorowicz retweeted
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/…
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