Entering edit mode
13.2 years ago
jli99
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150
I saw there are trimming options in both phred and phrap. I wonder what is the difference? And is there a general recommendation about whether and how to use trimming with phred phrap?
This is basically correct except that in general, phred should be used to output quality scores but not to trim (at least if reads are destined for phrap assembly). I would study the docs carefully: phred - http://www.phrap.org/phredphrap/phred.html and phrap - http://www.phrap.org/phredphrap/phrap.html, for details of command-line options and discussion of trimming and quality.