How genome complexity can explain the difficulty of aligning reads to genomes

BMC Bioinformatics

Table 4 Precision and recall averaged across 100 genomes at read lengths 50, 75, 100.

	Prec-50	Rec-50	Prec-75	Rec-75	Prec-100	Rec-100
Bowtie2	0.9871	0.9062	0.9943	0.9721	0.9965	0.9891
BWA-SW	0.9886	0.8983	0.9952	0.9831	0.9972	0.9951
CUSHAW2	0.9882	0.9868	0.9956	0.9956	0.9975	0.9975
GASSST	0.9836	1.1109	0.9897	1.0339	0.9914	0.9757
Masai	0.9889	0.9861	0.9958	0.9903	0.9976	0.9790
mrFAST	0.9408	0.5700	0.9862	0.9166	0.9833	0.9268
SeqAlto	0.9875	0.8851	0.9956	0.9748	0.9976	0.9925
SHRiMP2	0.9892	0.9798	0.9958	0.9905	0.9975	0.9974
Smalt	0.9858	0.9714	0.9954	0.9944	0.9974	0.9974
SOAP2	0.9893	0.9025	0.9959	0.7904	0.9976	0.6526

ISSN: 1471-2105