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

Table 2 A comparison of the BLASR, BWA-SW, and BLAT methods on E. coli reads

Method	Number of aligned reads	Number of aligned bases	Run time
BLASR-SA	94057	230.8 M	20m 54s
BLASR-BWT	94527	230.1 M	33m 57s
BWA-SW	97729	132.4 M	434m 5s
BLAT	99530	181.7 M	4724m 40s

Each method was used to align 48× coverage of reads from E. coli O104:H4. BLASR-SA uses a suffix array index of the genome, while BLASR-BWT uses a BWT-FM index of the genome.

ISSN: 1471-2105