Compressed q-Gram Indexing for Highly Repetitive Biological Sequences

Abstract

The study of compressed storage schemes for highly repetitive sequence collections has been recently boosted by the availability of cheaper sequencing technologies and the flood of data they promise to generate. Such a storage scheme may range from the simple goal of retrieving whole individual sequences to the more advanced one of providing fast searches in the collection. In this paper we study alternatives to implement a particularly popular index, namely, the one able of finding all the positions in the collection of substrings of fixed length ($q$-grams). We introduce two novel techniques and show they constitute practical alternatives to handle this scenario. They excel particularly in two cases: when $q$ is small (up to 6), and when the collection is extremely repetitive (less than 0.01% mutations).