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Old 10-28-2014, 08:19 AM   #5
Junior Member
Location: Netherlands

Join Date: Feb 2014
Posts: 3

Thank you for your response. Sorry for the confusion, but with the sentence about the speed I meant that MegaBLAST is much faster. I also measured Mauve by the way.

Tested with two bacterial samples (+/- 4.2MB) with five runs. See below average durations and the sum of all coverages (can exceed 100% because some regions are aligned at multiple locations):

- NUCmer: 15.52 s / 98.27%
- Mauve: 82.40 s / 103.60%
- MegaBLAST: 4.86 s / 100.91%
- BLASTn: 33.02 s / 122.36%

Speed is important for this project, but not crucial. The thing is though that MegaBLAST is faster, but also more sensitive.. Which makes me wonder why people nowadays still choose NUCmer instead of MegaBLAST.
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