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):
- grep/tr/wc: 0m 0.609s
- pyGATB: 0m 0.663s
- readfq: 0m 0.976s