Table 4

Performance of TopHat2 and other spliced aligners on paired reads in which at least one of the reads contained insertions and deletions (indels) of 1 to 3 bp.

Pairs with true indels (2,754,313)a

Pairs with sequencing-error indels (2,934,043)a


Program

Accuracy, %

Accuracy on 685,937 pairs with boundary indels, %b

Accuracy, %

Accuracy on 695,771 pairs with boundary indels, %b


TopHat2

+ Bowtie1

69.8

16.3

14.0

3.1


TopHat2 + Bowtie2

62.3

24.0

60.8

19.8


GSNAP

77.0

63.8

77.8

64.8


RUM

60.3

34.3

61.3

36.0


MapSplice

25.5

3.4

25.0

3.2


STAR

53.4

19.2

54.9

21.4


aThe number of pairs 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 pairs 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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