Posts tagged ‘shell’

• The FASTQ file format for sequences - September, 2008
  software, shell, EST

  The FASTQ format is the format of choice for most new sequencing technologies. Here, we implement a Haskell parser, and look at some ..uh, interesting properties of the format and its implementations.
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• Functional bash bracketing - July, 2008
  software, shell, EST

  My current development project is an EST pipeline. For various reasons, it is implemented in shell --- bash, to be exact. In other words, the pipeline is a script, or rather a set of scripts, that will tie together the various stages: masking, clustering, assembly, and annotation.
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