Pseudogenome Suffix Array

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.

PgSA is in general a free compression program available in both binary and source code releases.

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