Table 1

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

Program

No. of mapped reads

Correctly mapped reads, %

Incorrectly mapped reads, %

Unmapped reads, %

Correct junction reads, %^a

Correct short-anchored reads, %^b

TopHat2 + Bowtie1

19,826,638

98.31

0.82

0.87

95.28

93.69

TopHat2 + Bowtie2

19,826,673

98.03

1.10

0.87

94.28

89.67

TopHat1.14

19,616,874

94.64

3.45

1.91

84.44

44.08

GSNAP

19,997,255

94.21

5.77

0.02

83.15

26.01

RUM

19,555,823

88.11

9.67

2.22

65.35

8.59

MapSplice

19,872,372

97.28

2.08

0.64

92.09

75.57

STAR

19,087,508

92.14

3.30

4.56

77.17

3.54

^aThere were 6,862,278 reads spanning one or more splice junctions; the alignment accuracy of junction reads refers to this set.

^bThere were 1,448,022 reads extending 10 bp or less into one exon; the alignment accuracy of the short-anchored reads is based on these alignments.

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