Table 1

Benchmark results of short reads alignment programs.

Unspliced alignment

Spiced alignment


Program

True positive (%)

False positive (%)

Running time

(s)

True positive (%)

False positive (%)

Running time

(m)


SHRiMP

94.79

8.97

809

N/A

N/A

N/A

SeqMap

96.50

6.71

447

N/A

N/A

N/A

SOAP

96.41

6.72

101

N/A

N/A

N/A

MAQ

96.53

6.73

138

N/A

N/A

N/A

Qpalma

N/A

N/A

N/A

85.17

4.45

557


MapNext

96.51

6.72

209

83.89

4.31

231


A total of 1893118 reads (35 bp length, 134274 spliced and 1758844 unspliced) from 5796 coding DNA sequences of chromosome I of Arabidopsis thaliana for the query dataset were simulated. Accuracy measures were calculated under the same threshold by allowing at most two mismatches. For the unspliced alignment, the true and false positive rates equal the number of short reads with correct and incorrect alignment positions divided by 1758844, respectively. For the spliced alignment, the true and false positive rates equal the number of short reads with correct and incorrect alignment positions divided by 134274.

Bao et al. BMC Genomics 2009 10(Suppl 3):S13   doi:10.1186/1471-2164-10-S3-S13

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