Table 1: GNUMAP parameter tuning using the FM-index. The FM-index allows for much more exibility in regards to parameter tuning for read mapping. Here, we compare the GNUMAP with the hashmap to the FM-index with various parameters tuned. Tuning the parameters in GNUMAP-FM greatly increases the number of reads mapped while decreasing the run-time and amount of memory and maintaining mapping accuracy.
| Indexing Algorithm | k | Max Kmer Occ | Min Kmer Hits | Kmer Jump Size | All Read Accuracy | Mapped Read Accuracy | Run-Time (seconds) | Percent Reads Mapped |
|---|---|---|---|---|---|---|---|---|
| Hashmap | 15 | 1000 | 2 | 1 | 90.33% | 96.54% | 59.773 | 93.57% |
| FM-index | 15 | 1000 | 2 | 1 | 95.12% | 95.79% | 197.516 | 99.30% |
| 15 | 500 | 2 | 1 | 94.97% | 95.79% | 140.912 | 99.14% | |
| 15 | 200 | 2 | 1 | 94.64% | 95.82% | 92.796 | 98.76% | |
| 15 | 100 | 2 | 1 | 94.21% | 95.89% | 71.718 | 98.24% | |
| 15 | 50 | 2 | 1 | 93.59% | 95.90% | 56.733 | 97.59% | |
| 15 | 25 | 2 | 1 | 92.73% | 96.63% | 43.153 | 96.63% | |
| 15 | 10 | 2 | 1 | 90.94% | 96.27% | 26.073 | 94.46% | |
| 19 | 50 | 2 | 1 | 94.41% | 95.88% | 20.874 | 98.46% | |
| 19 | 10 | 2 | 1 | 93.20% | 96.06% | 15.712 | 97.02% | |
| 23 | 10 | 3 | 1 | 93.89% | 96.06% | 14.335 | 97.81% |