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Table 3 Mapping performance for a dataset of 1.48 million 454 reads.

From: Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing

Aligner Execution time (Hrs) % reads mapped uniquely
BLAT 84.5 94.1
BWA-SW 1.8 89.8
Pash high 5.4 96.2
Pash med 3.0 95.9
Pash low 2.4 95.7
Pash 3.0 fast 1.8 96.1
SSAHA2 14.3 96.9
  1. Execution time, in hours, and percent of reads uniquely mapped with at least 90% identity. Pash 3.0 is run with four different sensitivity settings: high, medium, low, and fast. SSAHA2 is run with the -454 flag, and BLAT is run with default parameters (tile size 11, requiring 2 seeds for a match). Pash is 2.6 to 7.9 times faster than SSAHA, with a sensitivity loss of 0.7-1.2%. Pash is 15-47 times faster than BLAT.