BLASR (Basic Local Alignment with Successive Refinement) is used 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. 


  • Website
  • Chaisson M and Tesler G (2012) “Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application.” BMC Bioinformatics 13:238. doi:10.1186/1471-2105-13-238
  • GitHub repository


Usage on Bridges


To see what other modules are needed, what commands are available and how to get additional help type

module help blasr


To see what versions of BLASR are available type

module avail blasr


To use BLASR, include a command like this in your batch script or interactive session to load the BLASR module:

module load blasr

Be sure you also load any other modules needed, as listed by the module help blasr command.