Table 3

A comparison of the BLASR, and BWA-SW methods on simulated reads
Method Correctly mapped Incorrectly mapped Skipped Runtime Memory
reads bases reads bases reads footprint
E. coli
BLASR-SA 108789 266.5M 229 0.38M 3766 48m 18s 202 MB
BLASR-BWT 108795 265.3M 259 0.45M 3604 59m 39s 46 MB
BWA-SW 111192 261.9M 1835 0.91M 3005 223m 57s 190 MB
H. sapiens
BLASR-SA 41726 102.3M 1074 1.89M 413 92m 26s 14.7 GB
BLASR-BWT 41582 101.7M 1159 1.75M 472 53m 26s 8.1 GB
BWA-SW 40381 96.3M 292 1.16M 1554 105m 24s 4.2 GB

Reads are simulated from E. coli and H. sapiens with length and accuracy parameters modeled from real reads from E. coli. Skipped reads are either marked as filtered in the SAM output, or missing from the output.

Chaisson and Tesler

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

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