ONeSAMP3.0

ONeSAMP 3.0 computes the effective population size of genomic data sets. This program takes a file in GENEPOP format and computes five summary statistics. The software then uses linear regression based on these summary statistics to estimate of effective population size.

It is strongly recommended that users read the accompanying manuscript before applying ONeSAMP to their data.

Usage Overview

1. The program can be executed on LINUX system.

2. Must have R downloaded in order to run the software

   You can download and set up the R environment at this link:

    https://www.tutorialspoint.com/r/r_environment_setup.htm
   

3. Python 3.8 or later is required to run the program

Getting Started

1. Make a new ONeSAMP directory

    mkdir ONeSAMP
    cd ONeSAMP
   

2. Clone the repository

    git clone https://github.com/AaronHong1024/ONeSAMP_3.git
   

3. Give the Permission to the ONeSAMP file under the build directory

    chmod 777 build/OneSamp
   

Running ONeSAMP

usage: python main [--s number of trails] [--o input]

positional arguments:
   input  input file name

optional arguments:
    --n     Flag for Monomorphic loci (default: False)
    --m     Minimum Allele Frequency (size: 0-1)
    --r     Mutation Rate (size: 0-1)
    --lNe   Lower of Ne Range (size: 10-)
    --uNe   Upper of Ne Range (size: -500)
    --lT    Lower of Theta Range (size: 1-)
    --uT    Upper of Theta Range (size: -10)
    --s     Number of ONeSAMP Trials (size: 1000-50000)
    --lD    Lower of Duration Range (size: 2-)
    --uD    Upper of Duration Range (size: -8)
    --i     Missing data for individuals (size: 0-1)
    --l     Missing data for loci (size: 0-1)

Run the program

    python main --s 1000 --o exampleData/genePop10Ix30L > output.txt

Getting Help

If you have any issues or anyquestions, please feel free to contact us at [email protected] or through the GitHub Issues.

Citing ONeSAMP

If you use the ONeSAMP in your research project, please cite:

Hong, A., Cheek, R.G., Mukherjee, K., Yooseph, I., Oliva, M., Heim, M., Funk, W.C., Tallmon, D. and Boucher, C., 2023. ONeSAMP 3.0: Effective Population Size via SNP Data for One Population Sample.