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Table 2 Evaluation on simulated data

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

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
  1. 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