Table 2

Performance of TopHat2 and other spliced aligners on a set of 20 million pairs of 100-bp reads, simulated based on transcripts from the entire human genome.

Program

No. of mapped pairs

Correctly mapped pairs, %

Incorrectly mapped pairs, %

Unmapped pairs, %

Correct junction pairs, %a

Correct short-anchored pairs, %b


TopHat2 + Bowtie1

19,683,426

96.70

1.72

1.58

93.31

90.09


TopHat2 + Bowtie2

19,686,006

96.19

2.24

1.57

92.03

85.88


TopHat1.14

19,219,055

89.57

6.53

3.90

78.36

40.39


GSNAP

19,999,867

88.84

11.16

0.00

76.55

22.87


RUM

19,869,579

79.07

20.28

0.65

56.28

8.42


MapSplice

19,342,087

92.03

4.68

3.29

86.53

72.48


STAR

19,951,620

85.21

14.55

0.24

68.94

3.16


aThere were 9,491,394 pairs of reads classified as junction pairs.

bThere were 2,702,624 pairs containing short-anchored reads.

Kim et al. Genome Biology 2013 14:R36   doi:10.1186/gb-2013-14-4-r36

Open Data