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Table 6 Simulated paired-end reads: search time and percent of correct alignments.

From: A random-permutations-based approach to fast read alignment

   Low indel probability High indel probability
Mismatch probability 1% 2% 5% 1% 2% 5%
Software Time/%Correct       
Bowtie
-v 3
time (s)
%correct
1766
91.8
2274
69.3
3068
6.1
1849
83.2
2375
63.8
3059
5.7
Bowtie
-v 3 -k 10
time (s)
%correct
6161
93.6
5283
70.5
3260
6.1
5793
84.9
5151
64.9
3246
5.8
Bowtie
-v 2
time (s)
%correct
241
79.7
333
42.2
353
1.3
256
73.2
337
39.6
352
1.2
Bowtie
-n 2
time (s)
%correct
483
86.4
593
64.8
645
50.4
486
78.4
618
59.6
664
46.1
Bowtie
-n 2 -k 10
time (s)
%correct
1308
87.8
1293
65.7
1054
51.1
1283
79.6
1199
60.5
1036
46.8
Bowtie2
-very-fast
time (s)
%correct
757
98
715
94.6
506
67.0
734
98.0
670
94.6
484
67.0
Bowtie2
-fast
time (s)
%correct
834
98.1
800
94.8
571
67.5
804
98.1
750
94.8
551
67.5
Bowtie2
-sensitive
time (s)
%correct
1104
98.4
1079
97.5
893
83.8
1062
98.4
1014
97.5
857
83.8
Bowtie2
-very-sensitive
time (s)
%correct
2070
98.5
2045
98.3
1671
96.5
2080
98.5
1968
98.3
1648
96.5
BWA
-o 0
time (s)
%correct
1026
99.1
1404
98.7
1670
78.1
1162
98.6
1379
98.0
1676
76.3
BWA
-o 1
time (s)
%correct
1252
99.1
1956
98.8
3062
78.4
1499
99.1
2274
98.8
3180
78.0
Permutations-based
(report one)
time (s)
%correct
155
98.2
208
97.9
300
95.0
166
97.6
223
97.2
313
93.6
Permutations-based
(report more)
time (s)
%correct
227
99.5
328
99.2
530
96.5
268
98.9
365
98.5
553
95.2
  1. The "low indel probability" datasets were generated with mutation rate: 0.1%, and indel ratio: 15%. The "high indel probability" datasets were generated with mutation rate: 0.1% and indel ratio: 100%. Each of the datasets contains 106 pairs of 100 character-long reads.
  2. For each dataset and each program, we report the search time (for BWA: overall run time) and the percent of the reads which were aligned to the correct position in the genome.
  3. In some cases and in some settings, the programs may report several possible alignments for some reads. When needed, additional filtering can be added to aligners in order to eliminate some of the results, as appropriate for specific applications. In the experiment, the programs reported < 3 alignments/read (in average, in sensitive modes), with 0-1 alignments for the majority of reads. In this table, when the program produces multiple possible alignments, it is enough that one of the reported alignments corresponds to the correct location in order to consider the alignment correct.