Table 2: GNUMAP using hashmap and FM-index comparison using the same mapping parameters. Run-time and number of mapped reads using the hashmap and FM-index versions of GNUMAP on the ART generated synthetic dataset and on the real dataset. As kmer size increases, from 7 to 10, run-time is about the same. For kmers sizes 11 and 12 run-time is much larger (see bolded rows). The run-time increase for these kmers is caused by the composition of hg19 where lots of 11 and 12-mers (13-mers in real dataset where 11 and 12-mers didn't finish) happen to have frequencies near the chosen threshold (1,000) resulting in more NW alignments that are costly in terms of time. For 13-mers and larger kmers, the run-time decreases and eventually settles at a minimum run-time.
Hashmap | FM-Index | |||
---|---|---|---|---|
k k |
Run-Time (HH:MM) |
Mapped Reads |
Run-Time (HH:MM) |
Mapped Reads |
7 | 0:52 | 0% | 0:06 | 0% |
8 | 0:53 | 0% | 0:06 | 0% |
9 | 1:01 | 0.17% | 0:18 | 0.02% |
10 | 1:30 | 1.89% | 1:34 | 1.63% |
11 | 10:08 | 46.51% | 7:03 | 44.76% |
12 | 7:14 | 70.68% | 5:10 | 70.57% |
13 | 3:38 | 69.82% | 2:08 | 69.81% |
14 | 1:19 | 65.65% | 0:55 | 65.65% |
15 | 1:09 | 59.50% | 0:30 | 59.50% |
16 | - | - | 0:21 | 55.26% |
17 | - | - | 0:17 | 55.21% |
18 | - | - | 0:15 | 55.38% |
19 | - | - | 0:14 | 55.05% |
20 | - | - | 0:12 | 55.59% |
21 | - | - | 0:11 | 48.85% |
22 | - | - | 0:10 | 44.68% |
23 | - | - | 0:10 | 40.57% |
(b) Real Dataset.
Hashmap | FM-Index | |||
---|---|---|---|---|
k k |
Run-Time (HH:MM) |
Mapped Reads |
Run-Time (HH:MM) |
Mapped Reads |
7 | 3:56 | 0% | 0:30 | 0% |
8 | 3:45 | 0% | 0:30 | 0% |
9 | 4:12 | 0.65% | 0:45 | 0.08% |
10 | 5:04 | 6.48% | 4:43 | 5.80% |
11 | - | - | - | - |
12 | - | - | - | - |
13 | 20:57 | 91.04% | 10:57 | 91.03% |
14 | 14:36 | 91.48% | 5:04 | 91.48% |
15 | 8:50 | 91.71% | 2:59 | 91.71% |
16 | - | - | 2:10 | 91.88% |
17 | - | - | 1:51 | 92.07% |
18 | - | - | 1:43 | 92.23% |
19 | - | - | 1:34 | 92.32% |
20 | - | - | 1:29 | 92.36% |
21 | - | - | 1:23 | 92.36% |
22 | - | - | 1:19 | 92.36% |
23 | - | - | 1:15 | 92.31% |