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Table 2 Statistics on real human datasets

From: Fast and SNP-aware short read alignment with SALT

Aligner Arg Sen (%) Acc (%) Uniq (%) Unmapped T1 T4
dataset 1: real-100
 SALT.snp -r 21 99.15 99.76 90.43 33,981 9 m 37 s 2 m 37 s
-r 10 99.24 99.76 90.19 30,341 11 m 41 s 3 m 8 s
-r 5 99.27 99.76 90.09 29,380 13 m 24 s 3 m 38 s
 SALT.linear -r 21 99.13 99.76 90.51   9 m 30 s 2 m 26 s
-r 10 99.23 99.76 90.29 30,619 10 m 34 s 2 m 52 s
-r 5 99.26 99.76 90.21 29,478 11 m 37 s 3 m 16 s
 BWA-MEM   99.99 97.59 91.60 374 18 m 59 s 5 m 42 s
dataset 2: real-148
 SALT.snp -r 21 97.39 99.95 89.35 104,347 18 m 13 s 4 m 35 s
-r 10 97.44 99.94 89.30 102,474 19 m 45 s 6 m 23 s
-r 5 97.47 99.94 89.21 101,457 26 m 34 s 7 m 25 s
 SALT.linear -r 21 97.38 99.96 89.49 104,839 14 m 14 s 3 m 47 s
-r 10 97.43 99.95 89.47 102,905 19 m 38 s 5 m 12 s
-r 5 97.46 99.95 89.39 101,795 25 m 20 s 6 m 40 s
 BWA-MEM   99.51 97.28 93.55 19,450 23 m 18 s 6 m 29 s
  1. SALT.linear and SALT.snp seed alignments with a linear reference and an SNP-augmented reference, respectively
  2. SALT selects seeds in reads every X nt with the setting “-r X”
  3. T1 and T4 are escaped time with 1 thread and 4 threads, respectively
  4. Best results are shown in bold