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Barley Pangenome Visualisation Suite

The graphical barley pangenome pipeline provides an interactive and comprehensive suite of visualisation and analytical tool integrating the multi-domain resources derived from the international barley pangenome project.

 

The Goal - Effective and Easy Analysis of Large Pangenome Projects

Our goal is to develop a comprehensive and interactive pangenome visualisation suite which enables easy exploration and analysis of the complex barley pangenome data, including genomics data, transcriptome data, and QTL data. There has been a critical need for such an analytical software from breeders and genetic scientists and our suite was developed with the specific requirements from users in mind. 
Our graphical pangenome suite integrates a number of software packages, including adapted existing tools and newly developed packages. Our software suite provides flexible analyses at different levels and purposes. Exploring genetic variations at either chromosome or gene levels, correlating genetic variations to traits and cross-linking genetic markers to physical genetic variations to identify key genes and variations regulating phenotypes. 
Our software suite was designed for large and complicated crop genomics applications, e.g. wheat, barley, oats, etc, yet it can be applied to other organisms with smaller and simpler genomes, such as bacteria and viruses.

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Genetic Map Visualisation

We developed an interactive tool for genome visualisation and comparison of SNPs, genes, and QTL data across multiple genomes and made cross-linking physical map and genetic map a breeze. This tool, Pretzel, can be readily used separately for other crops as wheat, lupin, oats, etc.

Genomic Variation Visualisation

We integrate several software tools to provide interactive representation of all kinds of genomic variations within the barley pangenome at both chromosome level and gene level. Specific haplotypes of the pangenome can be identified. Our software allows queries, including gene ID and sequences, to quickly narrow down the interested regions.

Genomic Functions and Transcriptomics Visualisation

Associative analyses between genetic variations and gene expression is straight-forward with our functional visualisation component. The downstream enriched functional pathways and gene clusters analyses can also be achieved with click of a button. Users can add custom tracks and manipulate the contents to visualise.

 

Overview

Our pangenome visualisation suite integrates a number of tools and  comprises of 3 main functional components:

  1. Genomic Variation Visualisation component;

  2. Functional Visualisation;

  3. Genetic Map Visualisation component.

The overview of our pangenome visualisation suite are shown below. 

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The analysis becomes easy with real-time interactions

 

Contact

Western Crop Genetic Alliance, Murdoch University
90 South St, Murdoch WA6150

+61 9360 7519

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