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Table 2 Mapping time and percent of reads uniquely mapped for a 19.5 million 76 bp reads dataset.

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)

% of reads mapped uniquely

BWA

9.2

45.4

Pash 3.0 high

33.5

58.2

Pash 3.0 med

25.5

56.5

Pash 3.0 low

20.5

55.7

Pash 3.0 fast

10.7

59.3

SSAHA2

234

59.5

  1. Pash 3.0 is run with four different sensitivity settings: high, medium, low, and fast. BWA is run with default parameters. BWA is 1.2-3.6x faster than Pash 3.0, but Pash 3.0 maps 10-14% more of the input reads.
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BMC Bioinformatics

ISSN: 1471-2105

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