Group highlights

(For a full list of publications see below)

AGC: Compact representation of assembled genomes with fast queries and updates

High-quality sequence assembly is the ultimate representation of complete genetic information of an individual. AGC is a utility allowing to represent collections of genome sequences obtained in pangenome projects in a very compact form. It also allows to access any contig (or its part) in a fraction of a second.

S Deorowicz, A Danek, H Li

Bioinformatics 39, btad094 (2023)

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

J Khan, M Kokot, S Deorowicz, R Patro

Genome Biology 23, 190 (2022)

CoLoRd: Compressing long reads

M Kokot, A Gudys, H Li, S Deorowicz

Nature Methods 19, 441–444 (2022)

PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences

A Zielezinski, S Deorowicz, A Gudys

Bioinformatics 38, 1447–1449 (2022)

Kmer-db: instant evolutionary distance estimation

S Deorowicz, A Gudys, M Dlugosz, M Kokot, A Danek

Bioinformatics 35, 133–136 (2019)

KMC 3: counting and manipulating k-mer statistics

M Kokot, M Dlugosz, S Deorowicz

Bioinformatics 33, 2759–2761 (2017)

FAMSA: Fast and accurate multiple sequence alignment of huge protein families

S Deorowicz, A Debudaj-Grabysz, A Gudys

Scientific Reports 6, 33964 (2016)


Full List of publications