Structure/Faststructure
Overview
Structure is a package for investigating population structure using multi-locus genotype data. For faster but less accurate results for large datasets, fastStructure is also available.
Availability
| Cluster | Module/Version |
|---|---|
| BOSE | structure/2.3.3 faststructure/1.0.4 |
| BGSC | Not Available |
Note: You can simply use module load structure to activate the most recently installed version of this software.
Arguments / Options
This is a list of arguments for the Structure/Faststructure command that we wanted to highlight.
| Option | Description |
|---|---|
| --input | input genotypes |
| --output | output genotypes |
| --format | input file format |
| --full | output all parameters |
| --seed | specify random number generator seed |
Sample Slurm Script
submit.sh
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]
# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32 # How many CPU cores do you want to request
#SBATCH --nodes=1 # How many nodes do you want to request
# -- SCRIPT COMMANDS -- #
# Load the needed modules
module load Structure/Faststructure # Load Structure/Faststructure
python structure/faststructure.py # Run the structure program. See official documentation for details.
Real Example
Has your research group used Structure/Faststructure in a project? Contact the HPC Team and we'd be glad to feature your work.
Citation
Please include the following citation in your papers to support continued development of Structure/Faststructure.
Citation Here