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Old 11-09-2011, 04:34 AM   #1
NicoBxl
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Location: Belgium

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Default short read aligner with 3 mismatch and one gap allowed

Hi,

Is there an short read (~25 nt) aligner that lets you specify the number of mismatch and number of gaps (and maybe the maximum length of the gap ? ) ?

Thanks,

N.
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Old 11-09-2011, 08:07 AM   #2
Nicolas
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Bowtie2?
Novoalign?
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Old 11-09-2011, 11:26 AM   #3
zee
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Novoalign does support gap open and gap extension penalties. Finding the right balance of these with your data is something you might think about doing. The defaults are set quite conservatively as with most other tools that perform a similar function.
Also do remember that allowing more gaps/mismatches can potentially drop your specificity.
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