REFRESH Bioinformatics Group


PgSA—What is it?

Pseudogenome Suffix Array is a compact index for collections of reads from sequencing. It allows to ask for presence of k-mers in the reads.

Terms of use of PgSA

PgSA is in general a free compression program available in both binary and source code releases. More details can be found out on download page.


+ Kowalski, T., Grabowski, Sz., Deorowicz, S., Indexing arbitrary-length k-mers in sequencing reads, PLOS ONE, 2015; 10(7):1–16, 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.