308 citations · 462 across the 24 of their papers we have counts for
7 papers · 1 filter
A note on the longest common substring with -mismatches problem
Szymon Grabowski
The recently introduced longest common substring with -mismatches (-LCF) problem is to find, given two sequences and of length each, a longest substring …
KMC 2: Fast and resource-frugal -mer counting
Sebastian Deorowicz, Marek Kokot, Szymon Grabowski +1
Motivation: Building the histogram of occurrences of every -symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name…
Sampling the suffix array with minimizers
Szymon Grabowski, Marcin Raniszewski
Sampling (evenly) the suffixes from the suffix array is an old idea trading the pattern search time for reduced index space. A few years ago Claude et al. showed an alphabet sampli…
Multiple pattern matching revisited
Robert Susik, Szymon Grabowski, Kimmo Fredriksson
We consider the classical exact multiple string matching problem. Our solution is based on -grams combined with pattern superimposition, bit-parallelism and alphabet size reduct…
Disk-based genome sequencing data compression
Szymon Grabowski, Sebastian Deorowicz, Łukasz Roguski
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, si…
Two simple full-text indexes based on the suffix array
Szymon Grabowski, Marcin Raniszewski
We propose two suffix array inspired full-text indexes. One, called SA-hash, augments the suffix array with a hash table to speed up pattern searches due to significantly narrowed…