MONI: A Pangenomics Index for Finding MEMs

Recently, Gagie et al. proposed a version of the FM-index, called the r-index, that can store thousands of human genomes on a commodity computer. Then Kuhnle et al. showed how to build the r-index efficiently via a technique called prefix-free parsing (PFP) and demonstrated its effectiveness for exact pattern matching. Exact pattern matching can be leveraged to support approximate pattern matching but the r-index itself cannot support efficiently popular and important queries such as finding maximal exact matches (MEMs). To address this shortcoming, Bannai et al. introduced the concept of thresholds, and showed that storing them together with the r-index enables efficient MEM finding --- but they did not say how to find those thresholds. We present a novel algorithm that applies PFP to build the r-index and find the thresholds simultaneously and in linear time and space with respect to the size of the prefix-free parse. Our implementation called MONI can rapidly find MEMs between reads and large sequence collections of highly repetitive sequences. Compared to other read aligners -- PuffAligner, Bowtie2, BWA-MEM, and CHIC -- MONI used 2--11 times less memory and was 2--32 times faster for index construction. Moreover, MONI was less than one thousandth the size of competing indexes for large collections of human chromosomes. Thus, MONI represents a major advance in our ability to perform MEM finding against very large collections of related references. Availability: MONI is publicly available at https://github.com/maxrossi91/moni.

State Complexity of Neighbourhoods and Approximate Pattern Matching

The neighbourhood of a language [Formula: see text] with respect to an additive distance consists of all strings that have distance at most the given radius from some string of [Formula: see text]. We show that the worst case deterministic state complexity of a radius [Formula: see text] neighbourhood of a language recognized by an [Formula: see text] state nondeterministic finite automaton [Formula: see text] is [Formula: see text]. In the case where [Formula: see text] is deterministic we get the same lower bound for the state complexity of the neighbourhood if we use an additive quasi-distance. The lower bound constructions use an alphabet of size linear in [Formula: see text]. We show that the worst case state complexity of the set of strings that contain a substring within distance [Formula: see text] from a string recognized by [Formula: see text] is [Formula: see text].