BLASR is a software for mapping Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error.
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BMC Bioinformatics. 2012 Sep 19;13:238. doi: 10.1186/1471-2105-13-238.
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory.
Chaisson MJ, Tesler G.