A tool to process DNA Sequence files produced by Sequencers like the Roche/454 Titanium FLX.

The settings are configurable via a XML file.

Possible operations:

- load FASTA+QUAL files
- load files containing MID and Primer sequences for sorting
- allow "fuzzy" matching of MIDs and Primers with user-defined number of allowed mismatches
- filter
  - min. Sequence length
  - max. Number of Ns
  - average Quality
  - after-sort:
    - single MID
    - single Primer
- trimming:
  - quality
  - trim off MID and Primer
  - fixed points
  - at motif
- output
  - all in a single file, or files per MID, Primer, or MID-Primer combination
  - compression as zip, tar.gz and tar.bz
  
- other things that might come up…