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Integrated Genome Browser (IGB)
Integrated Genome Browser (IGB, pronounced "ig-bee") is a fast, feature-rich, open-source desktop genome browser thousands of researchers have used to explore and analyze genomic data. IGB has visual analytics features that help users better understand and interpret data, such as the ability to create coverage graphs, merge annotations, and scale data. Below, you'll find the process for visualizing MetaCerberus output in IGB.
Go to bioviz.org and click the "Install IGB" button in the top right. Then, click the red download button to get the most recent release of IGB for your operating system.
Before you can visualize MetaCerberus output, the genome used to run MetaCerberus will need to be added as a custom genome in IGB.
IGB supports many species and genome versions, not just the species shown on the start screen. To check whether a genome is available in IGB, click the Current Sequence tab and use the Species and Genome Version menus to look for your genome of interest.
However, if your genome is not available, you can still use IGB. Here's how:
- Select File > Open Genome from File... (or click the DNA icon in the Toolbar.)
- Select a sequence file to use as the reference genome (fasta or 2bit format).
- Enter Optional details: i. Enter Genus name ii. Enter the Species name iii. Enter the Variety as appropriate (strain/cultivar/accession) iv. Choose the Month of the genome release date v. Enter the Year in YYYY format.
- Click OK and wait for the genome to load.
Output files with a .gff extension can be viewed in IGB. See File Formats for a list of all currently supported file formats.
To open local files on your computer:
- Select File > Open File... or File > Open URL...
- Enter file name or URL
Alternatively, drag and drop local files from your file chooser into IGB.
NOTE: Some MetaCerberus output in the .gff file format will have a ##FASTA section at the bottom. Although this is a valid component of a .gff file, IGB does not currently have the logic to parse it and has thus been throwing an error when it encounters files with this section. We are working on adding that logic, but in the meantime, removing all text from that section down in your .gff file will fix the issue.