Posts tagged ‘parsing’

• Compressing biological sequences - June, 2011
  sequence analysis, SFF, 454, parsing

  As sequence data continue to grow exponentially in volume, compression is becoming more interesting. Here's a quick test of a couple of popular algorithms, and how to get improved compression rates by simple rearrangements of the data.
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• 454 sequencing and parsing the SFF binary format - November, 2008
  sequence analysis, SFF, 454, parsing

  Roche's 454 sequencing technology can produce biological sequence data on a scale that exceeds traditional Sanger sequencing by orders of magnitude. Due to the fundamentally different method used to generate the sequences, we would like to investigate the raw data and see if we can quantify -- and maybe also reduce the number or severity of -- errors. This means reading the binary SFF format. Below, we'll dissect the SFF format, and describe a Haskell implementation.
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