mpscan: Fast Localisation of Multiple Reads in Genomes

Abstract. With Next Generation Sequencers, sequence based transcriptomic or epigenomic assays yield millions of short sequence reads that need to be mapped back on a reference genome. The upcoming versions of these sequencers promise even higher sequencing capacities; this may turn the read mapping task into a bottleneck for which alternative pattern matching approaches must be experimented. We present an algorithm and its implementation, called mpscan, which uses a sophisticated filtration scheme to match a set of patterns/reads exactly on a sequence. mpscan can search for millions of reads in a single pass through the genome without indexing its sequence. Moreover, we show that mpscan offers an optimal average time complexity, which is sublinear in the text length, meaning that it does not need to examine all sequence positions. Comparisons with BLAT-like tools and with six specialised read mapping programs (like Bowtie or ZOOM) demonstrate that mpscan also is the fastest algorithm...

• Type: Conference
• Year: 2009
• Where: WABI
• Authors: Eric Rivals, Leena Salmela, Petteri Kiiskinen, Petri Kalsi, Jorma Tarhio
• Keywords: Algorithms, Exact Matching, Read Mapping, Read Mapping Task, WABI 2009