The dephd package
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.
- No changelog available
Properties
| Versions | 0.0, 0.1, 0.1.1, 0.1.3, 0.1.4, 0.1.5, 0.1.6 |
|---|---|
| Dependencies | base (>=3 && <5), bio (>0.4), bytestring, cmdargs (>=0.5), directory, process, regex-compat |
| License | GPL |
| Author | Ketil Malde |
| Maintainer | Ketil Malde <ketil@malde.org> |
| Category | Bioinformatics |
| Home page | http://malde.org/~ketil/biohaskell/dephd |
| Executables | fakequal, dephd |
| Uploaded | Mon Mar 21 19:07:02 UTC 2011 by KetilMalde |
| Distributions | NixOS:0.1.6 |
| Downloads | 834 total (93 in last 30 days) |
| Status | Docs not available [build log] Successful builds reported [all 1 reports] |
Downloads
- dephd-0.1.6.tar.gz [browse] (Cabal source package)
- Package description (included in the package)
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