Indexing Arbitrary-length K-mers in Sequencing Reads

Today’s must read paper is this one from the KMC group, who has done amazing work using minimizers. (h/t: Rob Patro) We also seem to have missed their other paper that seems quite interesting - [Grabowski S, Raniszewski M (2014). Sampling the suffix array with minimizers. Publicly available preprint arXiv:1406.2348v2].

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.