Skip to main content

Advertisement

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.

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

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