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Needed: Speed-optimized FASTA statistics script #7

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jorvis opened this issue Dec 29, 2013 · 0 comments
Open

Needed: Speed-optimized FASTA statistics script #7

jorvis opened this issue Dec 29, 2013 · 0 comments

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@jorvis
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jorvis commented Dec 29, 2013

One of the really common tasks when given a FASTA file is to find the following statistics:

  • Total sequence count
  • Total base count
  • GC content
  • Longest sequence
  • Shortest sequence
  • Mean sequence length
  • Median sequence length
  • N50
  • N90

While this is trivial itself, what can get more interesting is finding the method to do it that performs the best. Because this will be an important component of a few other projects, speed and proper error handling is important. Most apps assume python, but I'm up for implementations in whatever language will give the best results here as long as they don't open up a huge can of worms dependency-wise.

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