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Needed: Speed-optimized FASTQ statistics script #6

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jorvis opened this issue Dec 29, 2013 · 1 comment
Open

Needed: Speed-optimized FASTQ statistics script #6

jorvis opened this issue Dec 29, 2013 · 1 comment

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@jorvis
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jorvis commented Dec 29, 2013

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

  • total read count
  • total base count

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.

@jorvis
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jorvis commented Dec 29, 2013

Here is an example implementation which could serve as the starting point to improve upon:

https://github.com/jorvis/biocode/blob/master/fastq/fastq_simple_stats.py

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