example_config.yml

# This is an example configuration file. Whitespace is important.

# Settings pertaining to the library design
library:
    genome:
        num-genes: 500
        num-guides-per-gene: 5
        frac-increasing-genes: 0.02 # fraction of genes with a positive phenotype
        frac-decreasing-genes: 0.1 # fraction of genes with a negative phenotype

    guides:
        crispr-type: CRISPRn # either CRISPRi or CRISPRn
        frac-high-quality: 0.9 # fraction of high quality guides
        mean-high-quality-kd: 0.85 # mean knockdown by a high quality guide (CRISPRi only)

screen:
    type: facs # either facs or growth
    num-runs: 10 # how many independent runs

    representation: # integer value, how much larger are samples than the library
        - transfection: 100
        - selection: 100
        - sequencing: 100

# screen-type specific parameters

    bin-size: 0.25 # size of tail to sample from, must be between 0 and 0.5 (FACS only)
    std-noise: 1 # (FACS only)
    num-bottlenecks: 10 # (Growth only)