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

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

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.

ISSN: 1471-2105