igv
Software Description
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Info
Module Name
igv
Last Updated On
08/29/2023
Support Level
Secondary Support
Software Access Level
Open Access
Home Page
Documentation
Software Description
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
General Linux
To run this software interactively in a Linux environment use the commands:
module load igv
igv.sh
You can also launch IGV, a Java application, on your own computer by visiting the IGV homepage (user registration is required. IGV has a selection of genomes pre-loaded. If you are using your own computer you will need to move your bam file(s) to your own computer too. An alternative method is to login to a MSI computer with NX client and enter the following command in a terminal:
isub -q lab
Then, start a web browser, log in to Galaxy, and save your bam file(s) into a scratch folder if you just need them temporarily, or save them to your project space folder if you want to save them long term. Files left in scratch folder will be deleted automatically after two weeks.
Agate Modules
Default
2.16.1
Other Modules
2.10.2, 2.16.1, 2.3.47, 2.3.8, 2.3.9, 2.8.0
Mangi Modules
Default
2.16.1
Other Modules
2.10.2, 2.16.1, 2.3.47, 2.3.8, 2.3.9, 2.8.0
Mesabi Modules
Default
2.16.1
Other Modules
2.10.2, 2.16.1, 2.3.47, 2.3.8, 2.3.9, 2.8.0