Integrative Genomics Viewer (IGV)¶
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IGV Web¶
igv.js is an embeddable interactive genome visualization component. The source code for igv.js is available on github:
Documentation is available at:
Try it now with public data in Google Genomics:
IGV Desktop¶
IGV Desktop supports browsing of reads from the Google Genomics Reads API and also from BAM files in Google Cloud Storage. It implements an OAuth flow to facilitate access to private data in addition to public data.
Setup¶
- Install or upgrade IGV Deskop to ensure you have a recent version. IGV Desktop can be obtained from http://www.broadinstitute.org/software/igv/download
- Change preferences so that the Google menu is displayed. Choose menu item View -> Preferences and check the box next to Enable Google access.
- Log into Google. Choose menu item Google -> Login ... and follow the OAuth prompts.
View a Google Genomics ReadGroupSet¶
Choose menu item Google -> Load Genomics ReadGroupSet and enter the readGroupSet ID for the readGroupSet you wish to view. For example, a readGroupSet ID of CMvnhpKTFhD3he72j4KZuyc will display the reads for NA12877 from Illumina Platinum Genomes.
View a BAM from Google Cloud Storage¶
Choose menu item File -> Load from URL and enter the Google Cloud Storage path for the BAM you wish to view. For example, a path of gs://genomics-public-data/platinum-genomes/bam/NA12877_S1.bam will display the reads for NA12877 from Illumina Platinum Genomes.
Be sure to have a .bai file stored along side the .bam file you wish to view.