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

Table 1 Alignment performance comparison for simulated WGS reads.

Read Size (bp)	76			100			150			200			300
Aligner	Hrs	TPR	PPV	Hrs	TPR	PPV	Hrs	TPR	PPV	Hrs	TPR	PPV	Hrs	TPR	PPV
BLAT	15	84.0	97.8	25	86.3	98.7	52.3	87.8	99.4	87.9	88.5	99.6	191.0	89.1	99.7
BWA/BWA-SW	0.3	86.7	99	0.8	88.2	99.4	1.9	88.2	99.6	0.9	91	98.3	1.2	91.4	98.7
Pash 3.0 high	2.4	87.3	99.1	3.3	88.9	99.4	5.3	89.9	99.5	7.5	90.4	99.5	12.4	90.9	99.7
Pash 3.0 med	2	86.8	99.1	2.1	88.3	99.2	2.8	89.7	99.3	3.8	90.4	99.5	6.5	90.8	99.6
Pash 3.0 low	1.7	86.7	99.1	1.8	88.2	99.2	2.0	89.6	99.3	2.5	90.3	99.5	4.1	90.8	99.6
Pash 3.0 fast	0.7	86.3	98.1	0.8	88.0	98.5	0.9	89.2	98.9	1.1	90.3	99.6	1.0	90.7	99.5
SSAHA2	15.3	87.5	99.1	10.6	88.8	99.3	8.8	89.5	99.2	10.0	90	99.2	14.7	90.2	99.0

Execution time, in hours (Hrs), and percent of reads uniquely and correctly mapped to the original location (%U) are reported. Each dataset contains 1 million simulated reads. The read size varies from 76 to 300 bp. Pash 3.0 is run with three different sensitivity settings: high, medium, and low. BWA and BWA-SW are run with default parameters; SSAHA2 is run with the -454 flag, and BLAT is run with default parameters (tile size 11, requiring 2 seeds for a match). We report the true positive rate (TPR), defined as the overall percentage of correctly mapped reads relative to all the input reads, and the positive predictive value (PPV), which indicates what percent of all reported mappings are correct. TPR is a measure of sensitivity, and PPV is a measure of specificity.

ISSN: 1471-2105