M
Marek Kokot
Researcher at Silesian University of Technology
Publications - 18
Citations - 776
Marek Kokot is an academic researcher from Silesian University of Technology. The author has contributed to research in topics: Computer science & Sorting. The author has an hindex of 7, co-authored 14 publications receiving 543 citations.
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KMC 3: counting and manipulating k-mer statistics.
TL;DR: Deorowicz et al. as discussed by the authors introduced KMC3, a significant improvement of the former KMC2 algorithm together with KMC tools for manipulating k-mer databases, which is shown on a few real problems.
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KMC 2: fast and resource-frugal k-mer counting
TL;DR: This work presents a novel method for k-mer counting, on large datasets about twice faster than the strongest competitors (Jellyfish 2, KMC 1), using about 12 GB (or less) of RAM.
Posted Content
KMC 3: counting and manipulating k-mer statistics
TL;DR: This work introduces KMC3, a significant improvement of the former KMC2 algorithm together with KMC tools for manipulating k‐mer databases, a standard procedure in many bioinformatics applications.
Journal ArticleDOI
Kmer-db: instant evolutionary distance estimation.
TL;DR: Kmer‐db is a new tool for estimating evolutionary relationship on the basis of k‐mers extracted from genomes or sequencing reads that estimates distances between pathogens in <7 min (on a modern workstation), 26 times faster than Mash.
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Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
TL;DR: Cuttlefish as mentioned in this paper reduces the de Bruijn graph construction time from 4.5 days to 17-23 hours, using only 1.52Tbp white spruce reads.