Overview of the BLASR method. (A) Candidate intervals are found by mapping short, exact matches as shown by colored arrows. Either a suffix array or BWT-FM index of the genome are used to find the exact matches. Intervals are defined over clusters of matches and are ranked; intervals with score 3, 6, and 4 are shown. (B) Matches scoring above a threshold are aligned using sparse dynamic programming on shorter exact matches. (C) Alignments that have a high-scoring sparse-dynamic programming score are realigned by dynamic programming over a subset of cells defined using the sparse dynamic programming alignment as a guide.