From: Efficient alignment of pyrosequencing reads for re-sequencing applications
S. pneumoniae | E. coli | P. falciparum | |||||||
---|---|---|---|---|---|---|---|---|---|
time | % reads | bp/err | time | % reads | bp/err | time | % reads | bp/err | |
BWA-SW | 19m | 92.86 | 40 | 16m | 65.4 | 22 | 8m | 95.98 | 56 |
SSAHA2 | 6m | 92.86 | 41 | 5m | 65.4 | 23 | 68m | 98.45 | 57 |
Newbler | 11m | 92.95 | 47 | 11m | 65.55 | 24 | 12m | 97.72 | 60 |
Segemehl | 181m | 90.77 | 61 | 110m | 62.95 | 32 | 90m | 98.14 | 62 |
GASSST | 6m | 89.96 | 63 | 4m | 62.71 | 32 | 3m | 62.80 | 72 |
TAPyR 85 | 2m | 88.37 | 70 | 13m | 59.98 | 35 | 48s | 95.30 | 66 |
TAPyR 50 | 3m | 93.33 | 40 | 20m | 66.80 | 20 | 51s | 98.91 | 53 |
C. elegans | D. pseudoobscura | H. sapiens | |||||||
time | % reads | bp/err | time | % reads | bp/err | time | % reads | bp/err | |
BWA-SW | 51m | 61.05 | 19 | 58m | 95.80 | 19 | 6s | 98.25 | 58 |
SSAHA2 | 513m | 70.40 | 18 | 92m | 97.30 | 18 | 16s | 99.44 | 54 |
Newbler | 45m | 69.07 | 19 | 119m | 96.86 | 23 | 1m | 98.72 | 78 |
Segemehl | 249m | 68.10 | 23 | 339m | 90.98 | 28 | 52s | 96.41 | 89 |
GASSST | 9m | 58.50 | 27 | 22m | 82.80 | 30 | 1m | 83.61 | 93 |
TAPyR 85 | 31m | 55.59 | 35 | 7m | 85.91 | 30 | 1s | 95.13 | 96 |
TAPyR 50 | 31m | 73.30 | 15 | 7m | 97.05 | 19 | 2s | 99.63 | 60 |