@marekkoki
Joined September 2012
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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!

Scalable and unsupervised discovery from raw sequencing reads using SPLASH2

Nature Biotechnology - SPLASH2 speeds up analysis of sequence variation in massive datasets.

nature.com
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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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Marek Kokot retweeted
𝕐@nomad42120 Sep 2022
Recently the paper describing Cuttlefish 2 (led by @scarecrow00007 and in collaboration with @marekkoki and @sdeorowicz) was published in @GenomeBiology (genomebiology.biomedcentral.…). We're quite excited about Cuttlefish 2 and what it enables. (short 🧵) 1/

Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2

Genome Biology - The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity...

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

The K-mer File Format: a standardized and compact disk representation of sets of k-mers

AbstractSummary. Bioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here,

academic.oup.com
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Marek Kokot retweeted
𝕐@nomad4213 Feb 2022
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/cuttl…)! It's also available on bioconda (linux/OSX). Feedback welcome!

Release Cuttlefish 2.0.0 · COMBINE-lab/cuttlefish

New features Cuttlefish is now able to construct compacted de Bruijn graphs from short read sets, along with reference sequences. This is made possible through the design of a new algorithm, Cuttl...

github.com
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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.

GitHub - refresh-bio/KMC: Fast and frugal disk based k-mer counter: counts 55-mers in 36 gzipped...

Fast and frugal disk based k-mer counter: counts 55-mers in 36 gzipped FASTQ files totaling 614 GB (WGS paired-end reads of NA12878, Illumina HiSeq 2000) in under 1.5 h, using 12 threads, 32 GB of ...

github.com
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