biocode
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Needed: Speed-optimized FASTQ statistics script
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.
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