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Table 4 Simulated single-end reads: search time and percent of correct alignments

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

Read length 75 100 150
Mismatch probability 1% 2% 5% 1% 2% 5% 1% 2% 5%
Software Time/%Correct          
Bowtie
-v 3
time (s)
% correct
141
94.9
245
89.0
517
45.0
177
94.4
350
81.9
588
24.1
306
89.5
537
60.9
647
5.0
Bowtie
-v 2
time (s)
% correct
58
91.1
90
76.2
165
25.1
79
87.6
125
63.7
190
11.0
126
76.2
194
38.9
218
1.6
Bowtie
-n 3
time (s)
% correct
152
92.6
236
84.6
439
67.7
234
92.5
393
78.8
961
65.2
397
88.2
733
59.4
2430
41.9
Bowtie
-n 2
time (s)
% correct
108
93.1
161
85.7
286
69.6
170
93.0
264
79.7
609
67.0
294
88.6
514
59.9
1560
43.1
Bowtie
-n 2 -k 10
time (s)
% correct
873
96.2
869
88.7
1179
72.9
1242
95.3
1069
81.7
2377
69.2
1511
90.3
1243
61.0
3446
44.0
Bowtie2
-very-fast
time (s)
% correct
169
93.6
163
87.3
136
59.5
234
95.3
233
91.2
196
69.4
363
95.9
366
93.0
299
76.1
Bowtie2
-fast
time (s)
% correct
224
94.0
223
88.2
178
60.8
329
95.9
320
92.4
267
71.0
533
96.9
523
94.7
422
78.2
Bowtie2
-sensitive
time (s)
% correct
354
95.2
315
92.1
275
73.1
498
96.5
462
94.6
396
80.4
791
97.6
765
96.6
638
88.4
Bowtie2
-very sensitive
time (s)
% correct
776
95.7
734
94.2
611
83.6
1124
96.8
1056
95.8
851
89.1
1864
97.8
1730
97.3
1383
94.2
Bowtie2
-very sensitive -k 10
time (s)
% correct
1063
98.0
813
95.8
691
84.6
1743
98.4
1341
96.6
1165
89.9
3498
98.9
2775
97.6
2395
94.9
BWA
-o 0
time (s)
% correct
320
96.5
457
93.3
516
59.9
404
97.2
743
93.9
610
54.2
715
97.4
931
92.5
447
33.1
BWA
-o 1
time (s)
% correct
359
97.1
560
93.8
889
60.2
483
98.1
1007
94.7
1206
54.6
904
98.7
1513
93.6
1034
33.4
Permutations-based
(mode 1)
time (s)
% correct
53
97.5
76
95.8
106
84.5
56
98.4
90
97.5
118
89.0
76
98.5
98
98.0
112
91.3
Permutations-based
(mode 2)
time (s)
% correct
147
97.8
149
96.4
152
86.6
155
98.5
147
97.8
145
90.6
145
98.6
148
98.1
156
92.7
Permutations-based
(fast)
time (s)
% correct
31
93.7
43
88.5
62
64.1
33
95.8
46
91.5
64
66.9
45
96.9
51
93.3
72
69.4
  1. Each dataset contained 106 reads. Mutation rate: 0.1%, indel ratio: 15%.
  2. 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 < 4 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.