Analyze quality of nucleotide sequences.
dephd - A simple tool for base calling and quality appraisal.
Reads files in phd-format (phred output), either specified individually, or in a directory (use the --input-dirs option to read directories or --input-list to read from an index file). Can also read FASTA with an associated quality file.
Can trim according to Lucy or Phred parameters, can mask by quality, can plot graphs (via gnuplot) of sequence quality to a window, or to JPG/EPS files. Can categorize sequences according to overall quality. Also constructs files suitable for submission to dbEST. More information at http://blog.malde.org/index.php/2010/09/07/submitting-ests-upstream/.
Also provides fakequal, a utility to generate bogus quality values, which are sometimes needed by less flexible tools.
The Darcs repository is at http://malde.org/~ketil/biohaskell/dephd.