pyGATB speed test

A little test on counting nucleotides in the C.elegans genome is available on StackExchange: pyGATB is ranked second fastest tool.

Tested tools are: bioawk, shell pipeline (grep + tr + grep), pure python, biopython, readfq and pyGATB.

Top 3 fastest tools are as follows (real time value):

  1. grep/tr/wc: 0m 0.609s
  2. pyGATB: 0m 0.663s
  3. readfq: 0m 0.976s

Read more on StackExchange.

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