Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory.

ABSTRACT:

Background

Recent methods have been developed to perform high-throughput sequencing of DNA by Single Molecule Sequencing (SMS). While Next-Generation sequencing methods may produce reads up to several hundred bases long, SMS sequencing produces reads up to tens of kilobases long. Existing alignment methods are either too inefficient for high-throughput datasets, or not sensitive enough to align SMS reads, which have a higher error rate than Next-Generation sequencing.

Results

We describe the method BLASR (Basic Local Alignment with Successive Refinement) 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. The method is benchmarked using both simulated reads

SUBMITTER: Chaisson MJ 

PROVIDER: S-EPMC3572422 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature