A fast read alignment method based on seed-and-vote for next generation sequencing

BMC Bioinformatics

Table 2 Evaluation on simulated data

Tool	sTime(s)	sConf(%)	sErr(%)	pTime(s)	pConf(%)	pErr(%)
BWA-MEM-125	581	96.2	0.030	642	97.8	0.018
Subread-125	227	93.5	0.896	204	95.8	1.268
FSVA-125	170	93.5	0.014	150	95.4	0.041
Bowtie2-125	792	94.9	0.020	772	94.9	0.297
BWA-MEM-150	748	96.7	0.023	737	98.0	0.012
Subread-150	271	95.0	0.728	246	96.9	1.054
FSVA-150	188	95.0	0.014	173	96.2	0.035
Bowtie2-150	966	95.0	0.015	929	94.9	0.260

Except in the ‘Tool’ column, the left three columns starting with ‘s’ represent the performance on single-end data, and the right three columns starting with ‘p’ represent the performance on pair-end data. ‘sTime’, ‘sConf’, ‘sErr’ refer to time cost, confident mapping percent and error rate correspondingly for single-end data. In the first element of each row, such as ‘BWA-MEM-125’, the number 125 following the tool name BWA-MEM represents read length for this test. All the experiments were run on a single core Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz

ISSN: 1471-2105