copMEM: finding maximal exact matches via sampling both genomes

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Abstract
Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in parallel regimes, is not quite satisfactory. We present a new algorithm, copMEM, that allows to sparsely sample both input genomes, with sampling steps being coprime. Despite being a single-threaded implementation, copMEM computes all MEMs of minimum length 100 between the human and mouse genomes in less than 2 minutes, using 7 GB of RAM memory. https://github.com/wbieniec/copmem Supplementary data are available at Bioinformatics online.
Funding Information
  • Lodz University of Technology (501/12-24-1-5418)