GCATemplates available: no
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.
IGV is best viewed using the HPRC portal.
- Open your favorite web browser and go to portal.hprc.tamu.edu
- Log in using your NetID and password
- Select 'Interactive Apps'
- Select 'IGV'
- Adjust the 'Number of hours' as needed.
- Increase the 'Number of processors' to 20 for viewing large genomes
- Click the blue 'Launch' button
- Wait for your job to start and then click the the blue 'Launch noVNC in New Tab' button when it appears.
- Navigate within IGV to find preconfigured genomes at /scratch/datasets/IGV
- You can add your own genomes by creating a .fai index for your fasta file using samtools on the command line before launching IGV
- module load SAMtools
- samtools faidx my_genome.fasta
- When you are finished using IGV, click the red 'Delete' button in the 'My Interactive Sessions' section to stop the IGV job.