Marek Kokot

Recently, our SPLASH paper (nature.com/articles/s4158…) was published in NatBiotech. Now, we release its extended version, sc-SPLASH (biorxiv.org/content/10.110…), which allows reference-free analysis of single-cell data. It was a great experience to work with our collaborators on that!

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…

Recently the paper describing Cuttlefish 2 (led by @scarecrow00007 and in collaboration with @marekkoki and @sdeorowicz) was published in @GenomeBiology (genomebiology.biomedcentral.com/articles/10.11…). We're quite excited about Cuttlefish 2 and what it enables. (short 🧵) 1/

In this new Bioinformatics Application Note, we introduce a file format named KFF for efficiently storing kmers on disk. academic.oup.com/bioinformatics…

After quite a bit of CMake and clang-related work by @scarecrow00007, the cuttlefish 2 functionality has been stabilized on the main branch, and the cuttlefish 2 release has been tagged (github.com/COMBINE-lab/cu…)! It's also available on bioconda (linux/OSX). Feedback welcome!

A gift for holidays from the KMC team - new release (v.3.2) of our k-mer counter is ready for download from github.com/refresh-bio/KMC Novelties: KFF format support, fast histogram estimation, KMC lib (easy integration in C++ apps) and more.