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Old 09-24-2014, 01:28 AM   #3
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Location: Cambridge

Join Date: Aug 2014
Posts: 6

I don't have a lot of experience with the software mentioned, but I want to put in my two cents on error correction and quality filtering generally.
These two things are usually considered separate steps in the bioinformatic workflow, but in my mind they need to be considered at the same time, as it is difficult to make an accurate call about error-correction if you've already trimmed off your low quality base calls.

SAMtools will probably solve a lot of your problems when used in conjunction with more specialised modules, depending on whether you have a reference, etc.
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