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

From: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

  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
  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.