IGV is a genome viewer that is able to efficiently handle large heterogeneous datasets. The tool supports loading local and remote datasets, and provides high-performance concurrent visualization across hundreds of samples. IGV can render both indexed (BAM, Goby) and nonindexed (GFF, BED, WIG) file formats. Diverse data types can be sorted, filtered, and overlayed by any clinical/experimental annotations. IGV touts real-time pan and zoom as well as fast data loading times, while consuming minimal computer resources.

In this project the tools we mainly used was IGV. Other tools we may used in the future could include Amazon S3.

Take Me There

Supported formats to visualize are GFF3, MUT

In order to have the system properly link your tree with your GFF3 track data, your track naming format should replace all '/' and whitespace with '_'.

For example if the sample in your phylogenetic tree file you wish to visualize has a name of 'usa/region/test/samplename', then the GFF3 track file name should 'usa_region_test_samplename'.

1. Select Sample File

1. James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011)
2. Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics 14, 178-192 (2013).
3. James T. Robinson, Helga Thorvaldsdóttir, Aaron M. Wenger, Ahmet Zehir, Jill P. Mesirov. Variant Review with the Integrative Genomics Viewer (IGV). Cancer Research 77(21) 31-34 (2017)
4. James T. Robinson, Helga Thorvaldsdóttir, Douglass Turner, Jill P. Mesirov. igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). bioRxiv 2020.05.03075499.

We would like to offer our special thanks to:

1. Cindy Martin,Cyberinfrastructure Engineer,UTech Research Computing and Cyberinfrastructure, Case Western Reserve University,Cleveland, Ohio
2. Mike Warfe, Director,UTech Research Computing and Cyberinfrastructure, Case Western Reserve University,Cleveland, Ohio
3. Hadrian Djohari,HPC Service Manager, UTech Research Computing and Cyberinfrastructure, Case Western Reserve University,Cleveland, Ohio
4. E.M. Dragowsky,Computing Technologist,Scientist & Information Analyst, UTech Research Computing and Cyberinfrastructure, Case Western Reserve University,Cleveland, Ohio
5. Nasir Yilmaz,IT Engineer, UTech Research Computing and Cyberinfrastructure, Case Western Reserve University,Cleveland, Ohio

We would like to offer our special thanks to:

1. Cindy Martin,Cyberinfrastructure Engineer,UTech Research Computing and Cyberinfrastructure, Case Western Reserve University,Cleveland, Ohio
2. Mike Warfe, Director,UTech Research Computing and Cyberinfrastructure, Case Western Reserve University,Cleveland, Ohio
3. Hadrian Djohari,HPC Service Manager, UTech Research Computing and Cyberinfrastructure, Case Western Reserve University,Cleveland, Ohio
4. E.M. Dragowsky,Computing Technologist,Scientist & Information Analyst, UTech Research Computing and Cyberinfrastructure, Case Western Reserve University,Cleveland, Ohio
5. Nasir Yilmaz,IT Engineer, UTech Research Computing and Cyberinfrastructure, Case Western Reserve University,Cleveland, Ohio
6. Derek Li,Department of Computer and Data Sciences, Case Western Reserve University, Cleveland Ohio and the College at the University of Chicago, Chicago,IL
7. Erik A. Li, Department of Computer and Data Sciences, Case Western Reserve University, Cleveland Ohio and Solon High School, Solon, Ohio