From: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Length | Program | CPU time | Wall clock time | Peak virtual memory footprint (megabytes) | Bowtie speed-up | Reads aligned (%) |
---|---|---|---|---|---|---|
36 bp | Bowtie | 6 m 15 s | 6 m 21 s | 1,305 | - | 62.2 |
 | Maq | 3 h 52 m 26 s | 3 h 52 m 54 s | 804 | 36.7× | 65.0 |
 | Bowtie -v 2 | 4 m 55 s | 5 m 00 s | 1,138 | - | 55.0 |
 | SOAP | 16 h 44 m 3 s | 18 h 1 m 38 s | 13,619 | 216× | 55.1 |
50 bp | Bowtie | 7 m 11 s | 7 m 20 s | 1,310 | - | 67.5 |
 | Maq | 2 h 39 m 56 s | 2 h 40 m 9 s | 804 | 21.8× | 67.9 |
 | Bowtie -v 2 | 5 m 32 s | 5 m 46 s | 1,138 | - | 56.2 |
 | SOAP | 48 h 42 m 4 s | 66 h 26 m 53 s | 13,619 | 691× | 56.2 |
76 bp | Bowtie | 18 m 58 s | 19 m 6 s | 1,323 | - | 44.5 |
 | Maq 0.7.1 | 4 h 45 m 7 s | 4 h 45 m 17 s | 1,155 | 14.9× | 44.9 |
 | Bowtie -v 2 | 7 m 35 s | 7 m 40 s | 1,138 | - | 31.7 |