Indexing Arbitrary-Length k-Mers in Sequencing Reads.

Indexing Arbitrary-Length k-Mers in Sequencing Reads.

Tomasz Kowalski, Szymon Grabowski, Sebastian Deorowicz

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.

2015

DOI: 10.1371/journal.pone.0133198

PLoS ONE

Public Library of Science (PLoS)

Science, Medicine

EN