Fast and SNP-aware short read alignment with SALT

BMC Bioinformatics

Table 1 Statistics on simulated human datasets

Aligner	Arg	Sen (%)	Acc (%)	Uniq (%)	Unmapped	T1	T4
dataset 1: sim-70
SALT.snp	-r 21	99.48	94.15	86.87	20,803	8 m 56 s	2 m 12 s
	-r 10	99.50	94.18	86.69	19,922	10 m 26 s	2 m 29 s
	-r 5	99.54	94.24	86.49	18,382	12 m 56 s	3 m 1 s
SALT.linear	-r 21	99.46	94.15	86.88	21,682	9 m 54 s	2 m 23 s
	-r 10	99.48	94.18	86.71	20,602	10 m 14 s	2 m 38 s
	-r 5	99.53	94.23	86.52	18,617	11 m 59 s	2 m 38 s
BWA-MEM		100.00	93.83	92.29	60	11 m 56 s	2 m 59 s
dataset 1: sim-100
SALT.snp	-r 21	99.68	95.67	90.74	12,667	9 m 52 s	2 m 32 s
	-r 10	99.70	95.71	90.59	12,022	12 m 6 s	3 m4 s
	-r 5	99.70	95.72	90.51	11,829	15 m 4 s	3 m 51 s
SALT.linear	-r 21	99.68	95.67	90.78	12,817	9 m 6 s	2 m 23 s
	-r 10	99.70	95.71	90.64	12,067	10 m 51 s	2 m 48 s
	-r 5	99.70	95.72	90.56	11,856	13 m 3 s	3 m 32 s
BWA-MEM		100.00	95.34	93.54	1	14 m 11 s	3 m 36 s
dataset 2: sim-150
SALT.snp	-r 21	99.86	96.72	92.21	5448	12 m 52 s	3 m 20 s
	-r 10	99.87	96.73	92.22	5235	16 m 4 s	4 m 9 s
	-r 5	99.87	96.73	92.15	5151	21 m 16 s	5 m 25 s
SALT.linear	-r 21	99.86	96.72	92.32	5482	13 m 30 s	3 m 6 s
	-r 10	99.87	96.72	92.34	5265	14 m 19 s	3 m 43 s
	-r 5	99.87	96.73	92.28	5179	18 m 4 s	4 m 40 s
BWA-MEM		100.00	96.35	94.36	0	20 m 20 s	5 m 35 s

SALT.linear and SALT.snp seed alignments with a linear reference and an SNP-augmented reference, respectively
SALT selects k-mers in reads every X nt with the setting “-r X”
T1 and T4 are escaped time with 1 thread and 4 threads, respectively
Best results are shown in bold

ISSN: 1471-2105