Table 1.

Speedup due to targeted alignment

	NOTCH1		Cancer genes
Sample	1 core	4 cores	1 core	4 cores
RNA-seq (2 × 50 bp)	96	53	6.8	6.7
RNA-seq (1 × 75 bp)	92	25	4.5	4.0
Exome-seq (2 × 100 bp)	43	16	3.0	3.1
WG-seq (2 × 100 bp)	66	19	2.8	2.6

Speedups computed by comparing the time required to perform the full alignment and the combined time of triage classification plus mapping of the selected reads. For RNA-seq samples, target regions consisted of exons and 20 bp flanking sequences, s = 14 and H = 46. For exome and WG samples, which have longer reads, target regions consisted of exons and 85 bp flanking regions, s = 14 and H = 85. (Speedups are approximate with error; results may also vary depending on options used, background load, etc.)