Figure 9.

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.

Chaisson and Tesler BMC Bioinformatics 2012 13:238   doi:10.1186/1471-2105-13-238
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