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Execution times of the original and improved versions of LoFreq. In all cases the number of variants called was identical between versions. Note that while the true depth of the 25Gb file is likely around 5 million reads, LoFreq by default limits columns to 1 million.
| Input size | Avg. depth | Speed- up | |
|---|---|---|---|
| New | |||
| 58M | 1,000x | 51 (s) | 1.0x |
| 237M | 30,000x | 26 (m) | 2.6x |
| 935M | 100,000x | 4 (h) | 3.3x |
| 2G | 300,000x | 12 (h) | 4.6x |
| 25G | 1,000,000x | 111 (h) | 3.7x |
