2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2015
Abstrakt

Mark J. Chaisson, Glenn Tesler. Mapping single molecule sequencing reads using basic local alignment withsuccessive refinement (BLASR): application and theory. BMC bioinformatics, 13:238. 2012.

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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 and reads from a bacterial sequencing project. We also present a 
combinatorial model of sequencing error that motivates why our approach is
effective. CONCLUSIONS: The results indicate that it is possible to map SMS reads
with high accuracy and speed. Furthermore, the inferences made on the mapability 
of SMS reads using our combinatorial model of sequencing error are in agreement
with the mapping accuracy demonstrated on simulated reads.