title: Indexing Arbitrary-Length k-Mers in Sequencing Reads.
abstract: We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating k-mers in sequencing reads. Our solution, PgSA (pseudogenome suffix array), based on finding overlapping reads, is competitive to the existing algorithms in the space use, query times, or both. The main applications of our index include variant calling, error correction and analysis of reads from RNA-seq experiments.
authors.affiliation: Institute of Applied Computer Science, Lodz University of Technology, Al. Politechniki 11, 90-924 Łódź, Poland.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Kowalski
authors.affiliation: Institute of Applied Computer Science, Lodz University of Technology, Al. Politechniki 11, 90-924 Łódź, Poland.
authors.forename: Szymon
authors.initials: S
authors.lastname: Grabowski
authors.affiliation: Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Deorowicz
mesh_terms: D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D066264:Datasets as Topic; D004926:Escherichia coli / Q000235:genetics; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017423:Sequence Analysis, RNA / Q000379:methods / Q000706:statistics & numerical data*; D012984:Software