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

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.

ISSN: 1471-2105