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Natural Diversity Genotypes

This module provides support and visualization of genotypic data stored in a modified GMOD Chado schema. The 3.x branch of this module represents a shift towards support for large scale genotypic datasets through backwards compatible improvements to the Chado schema including a new gathering table for genotypes (genotype_call) modelled after the chado phenotype table, optimized queries and well-choosen indexes. For benchmarking demonstrating the efficiency of this module, see our documentation.

Dependencies

Tripal 3.x (Installation Instructions)
PostgreSQL 9.3 (9.4+ recommended; tested with 11.3)
Tripal D3.js & Drupal Libraries API
Tripal Download API

Installation

This module is installed by cloning it and it's dependencies in [your drupal site]/sites/all/modules and enabling it through the Drupal Administrative UI. Specifically, once you have a working Tripal environment:

drush pm-download libraries
drush pm-enable libraries -y
cd [drupal root]/sites/all/modules
git clone https://github.com/tripal/tripald3
git clone https://github.com/tripal/trpdownload_api
cd [drupal root]/sites/all/libraries
mkdir d3 && cd d3
wget https://github.com/d3/d3/releases/download/v3.5.17/d3.zip
unzip d3.zip
drush pm-enable trpdownload_api tripald3 -y
cd [drupal root]/sites/all/modules
git clone https://github.com/UofS-Pulse-Binfo/nd_genotypes.git
drush en nd_genotypes -y

Features

Extensive configuration allowing for flexiblity in ontology terms used, as well as, colours and wording used in visualizations.
Multiple Tripal 3 Fields which provide flexible, configurable summaries of genotypic data.
Genotype Matrix search allowing users to extract genotypes for a user-defined set of germplasm.
Integration of all fields with Tripal 3 web services allowing you to share your genotypic data with other groups.

See Demonstration for how to demonstrate these features on your test site with simulated data.

Documentation

Please visit our online documentation to learn more about installation, usage and features.

Funding

This work is supported by Saskatchewan Pulse Growers [grant: BRE1516, BRE0601], Western Grains Research Foundation, Genome Canada [grant: 8302, 16302], Government of Saskatchewan [grant: 20150331], and the University of Saskatchewan.

Citation

Sanderson, L.A. (2020). ND Genotypes: Large-scale Genotypic data integration with Tripal. Version 3.2. University of Saskatchewan, Pulse Crop Research Group, Saskatoon, SK, Canada. Zenodo, doi:10.5281/zenodo.3731337.

UofS-Pulse-Binfo / nd_genotypes

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