Structure Harvester
Structure Harvester parses the output of Pritchard's Structure program, applies the Evanno ΔK method to help detect the number of clusters, and can optionally emit CLUMPP-compatible indfiles and popfiles.
License
Free to use and open source under the MIT License.
Available
- Roihu: 0.7, via the
bio-appsmodule.
Usage
Structure Harvester is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the module:
Run structureHarvester.py on a directory of Structure result files:
Structure Harvester is often used as part of an automated Structure workflow — see StrAuto, which runs it as part of its post-processing.
Example batch script
#!/bin/bash
#SBATCH --job-name=structureharvester
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=2G
module load bio-apps/v202603
module load structureharvester/0.7
structureHarvester.py --dir=structure_results --out=harvester_out --evanno --clumpp
Replace <project> with your CSC project (for example project_2001234).
See creating a batch job script for Roihu for more information about running batch jobs.