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. 2016 Jan 5;23(2):93–100. doi: 10.1093/dnares/dsv039

Table 3.

Scalability with the number of reads

Million reads HPG Aligner HISAT STAR TopHat2+Bowtie2 MapSplice
2 0.9 0.95 4.5 38.7 11.8
5 1.9 1.7 5.6 40.5 18.65
10 3.8 4.2 7.75 75.2 36.4
20 7.6 7.28 13.5 112.2 68.5

Runtimes for producing a BAM file (in min) of the different aligners in datasets of growing size.