Overview
This section will provide some quick training on how to use JBrowse2. You can also learn more via the JBrowse2 User Guide.
With the switch to JBrowse2, we have decided that not all the genomes will get migrated to JBrowse2 and that going forward, we will focus on a select number of genomes from each crop (the genomes everyone use as references or are genetically diverse) and provide value-added analyses to these genomes that will facilitate genomic discovery. We will adjust the genomes available in JBrowse2 to fit the community needs.
Advantages of using JBrowse2 versus JBrowse1:
- Can view multiple genome chromosomes/scaffolds in one panel
- Can view multiple genomes in same session
- Can view synteny analysis results and relationships between genomes
- Can generate dot plots between two genomes that can be used to navigate to genome regions
- Can view pangenome data
Same features in JBrowse2 as JBrowse1:
- Can view annotated genes and mRNA for genome and can zoom to nucleotide level
- Can view aligned PCR-based markers and SNP markers and QTL
- Can search by gene, mRNA, marker, or trait names
Accessing JBrowse2
JBrowse2 can be accessed by clicking on the JBrowse link for the respective genome on the JBrowse page, or you can open an empty session with the link at the top of that page. If you are started with an empty session, click on "Linear Genome View" and select a genome of interest.
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Here are some basics for navigatign JBrowse2:
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