JBrowse 2 has the ability to display pairwise comparative data. At WormBase, we have comparative data between these species/assemblies:

• C. elegans N2
• C. elegans Hawaiian strain
• C. elegans VC2010
• C. brenneri
• C. briggsae
• C. inopinata
• C. japonica
• C. remanei 

These comparisons are made with minimap2 with the option to generate CIGAR strings. The CIGAR strings allow JBrowse to show the inserts and deletions between the compared genomes.  These pre-computed comparisons can be found in a few ways from WormBase’s JBrowse.

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Spreadsheet view

JBrowse 2 has a “spreadsheet view” that looks much like you might expect: a simple spreadsheet. The primary way a WormBase user might interact with the spreadsheet view is if you have a file that has a list of genomic locations that are of interest and you’d like to step through.  For example, consider this list of locations that have comments separated by a tab (so that this is a tsv file–JBrowse supports tsv, csv, VCF, BED and BEDPE files in the spreadsheet view:

  I:16,632..17,470     site 1
  I:314,852..315,768   site 2
  I:382,162..383,013   site 3--this is the good one
  I:397,470..398,755   site 4 

You can put this in the spreadsheet view by selecting “Spreadsheet view” from the Add menu:

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Searching in JBrowse 2 is quite similar to searching in JBrowse 1. The most common way you would look for a feature would be to type the name of a feature in the location field (that is, the field that has the current location in it, like this:

Anything that you could search for in JBrowse 1 you can search for in JBrowse 2, and there is a good reason for that: they are using exactly the same data and search indexes. So, you can look for gene and transcript names, identifiers like WBGene00006749, and allele names like pkP649.  Of course, you can also enter a location like II:100000..200000. The only difference in name searching between JBrowse 1 and 2 is that when you search for something, you will almost always get a message like this in the bottom of the screen:

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In JBrowse 2 there are multiple ways to obtain sequence information. One is via a context menu when region is selected by clicking and dragging on the “number line” part of the linear genome view:

Selecting “Get sequence” from the context menu will open a dialog where you will have a few options for how to get your sequence:

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