Table 2

A comparison of the BLASR, BWA-SW, and BLAT methods onE. colireads
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.

Chaisson and Tesler

Chaisson and Tesler BMC Bioinformatics 2012 13:238   doi:10.1186/1471-2105-13-238

Open Data