GitHub - brandstaetter/SequenceProcessing: Small tool that provides filtering, trimming, sorting, and statistics of DNA Sequence files

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Small tool that provides filtering, trimming, sorting, and statistics of DNA Sequence files

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Name		Name	Last commit message	Last commit date
Latest commit History 10 Commits
.settings		.settings
src		src
.classpath		.classpath
.gitignore		.gitignore
.project		.project
.travis.yml		.travis.yml
README		README
pom.xml		pom.xml

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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…