Can Phred automatically trim sequences?
Phred has several ways to calculate where low-quality sequence should be clipped; however, you will probably need to write a script to apply the clipping information. But if you are planning to use the entire package, including Consed, there is not need for clipping. The current version of Phred can calculate where low-quality sequence should be clipped, and to apply the trimming to output files generated by Phred. We suggest to use the -trim_alt option rather than the -trim option for trimming. Only -trim_alt allows you to adjust the trim stringency with the -trim_cutoff option. In general, you should not apply low quality clipping if you want to use Phrap for assembly – Phrap deals perfectly well with low quality ends. For more information about trimming, please visit http://www.codoncode.com/support/faqs/trimming.
