Table 3 Real single-end reads: search time
From: A random-permutations-based approach to fast read alignment
Software | Search time (s) | ||
|---|---|---|---|
| Â | SRR023337_1 78 bp | ERR009392_1 108 bp | ERR016249_1 160 bp |
Bowtie -v 3 | 233 | 256 | 773 |
Bowtie -n 2 | 144 | 334 | 1560 |
Bowtie -n 2 -k 10 | 658 | 1142 | 2830 |
Bowtie2 -very-fast | 179 | 285 | 440 |
Bowtie2 -sensitive | 328 | 654 | 853 |
Bowtie2 -very-sensitive | 812 | 1488 | 1855 |
Bowtie2 -very-sensitive -k 10 | 1121 | 2430 | 3869 |
BWA -o 0 | 548 | 860 | 2434 |
Permutations-based (mode 1) | 65 | 68 | 111 |
Permutations-based (mode 2) | 147 | 151 | 145 |
Permutations-based (fast) | 35 | 39 | 57 |