The dephd package

[Tags: gpl, program]

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.


Properties

Versions0.0, 0.1, 0.1.1, 0.1.3, 0.1.4, 0.1.5, 0.1.6
Dependenciesbase (>=3 && <5), bio (>0.4), bytestring, cmdargs (>=0.5), directory, process, regex-compat
LicenseGPL
AuthorKetil Malde
MaintainerKetil Malde <ketil@malde.org>
CategoryBioinformatics
Home pagehttp://malde.org/~ketil/biohaskell/dephd
Executablesfakequal, dephd
Upload dateMon Mar 21 19:07:02 UTC 2011
Uploaded byKetilMalde
Downloads331 total (31 in last 30 days)

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