BLASR

Mark Chaisson and Glenn Tesler,
Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application,
BMC Bioinformatics (2012), 13:238.
Published: 19 September 2012

Article at journal (doi:10.1186/1471-2105-13-238)

We describe the method BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion error. We also present a combinatorial model of sequencing error that motivates why our approach is effective. The results indicate that mapping SMS reads is both highly specific and rapid.

Blasr may be obtained from these sites:

• GitHub: Github repository
• Pacific Biosciences Developers' Network: As part of the the SMRT Analysis software suite. There is also an official Pacific Biosciences website for BLASR, including a video about it.

• E. coli O104:H4 reads produced on the Pacific Biosciences RS platform:
  Register for an account at the Pacific Biosciences website, www.smrtcommunity.com. After you are logged in, a direct link to download the dataset is here.
• E. coli O104:H4 reference genome at BGI.

M.C. is a full-time employee at Pacific Biosciences, a company commercializing single-molecule, real-time nucleic acid sequencing technologies. G.T. was partially supported by a grant from the National Institutes of Health, USA (NIH grant 3P41RR024851-02S1). Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the organizations or agencies that provided support for the project.