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helper_scripts.md

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Helper scripts

Various helpful utilities will be added to epic. Currently it includes:

epic-effective

A perennial question on bioinformatics sites is how to compute the effective genome size for a genome. epic includes a script called epic-effective to do just this. It can use multiple cores. Please share your results on the issue tracker.

And the script to compute the effective genome size has the following CLI:

epic-effective
Compute the effective genome size from a fasta file.

(Visit github.com/endrebak/epic for examples and help.)

Usage:
    epic-effective --read-length=LEN [--nb-cpu=CPU] FILE
    epic-effective --help

Arguments:
    FILE                      Fasta genome
    -r LEN --read-length LEN  length of reads

Options:
    -h --help                 show this help message
    -n CPU --nb-cpu CPU       number of cores to use [default: 1]