Table 3

Performance of TopHat2 and other spliced aligners on single-end reads containing insertions and deletions (indels) of 1 to 3 bp.

Reads with true indels (1,428,499)a

Reads with sequencing-error indels (1,525,657)a


Program

Accuracy, %

Accuracy on 351,465 reads with boundary indels, %b

Accuracy, %

Accuracy on 357,334 reads with boundary indels, %b


TopHat2

+ Bowtie1

70.9

16.8

12.1

2.8


TopHat2

+ Bowtie2

63.7

25.2

62.6

21.2


GSNAP

82.7

71.9

83.1

71.8


RUM

69.4

43.0

70.3

45.4


MapSplice

27.3

3.7

27.5

3.8


STAR

46.6

16.9

47.7

17.1


aThe number of reads containing each type of error is indicated in the column header. bBoundary indels occur within 25 bp of an exon boundary. Percentages refer only to the reads of each type, not to the entire dataset.

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

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