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.
What'S The Difference Between Trimming In Phred And Phrap?
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Just glanced over the docs, looks like phred trimming is primarily based on base qualities, while phrap allows input of un-trimmed sequences and then decide whether to trim based not only on low qualities at ends and assembly situations. I think people that are more familiar with this assembly pipeline will give you a more definite answer.
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