The JBrowse genome browser has been around for a long time now. In fact, our first mention of it on the blog was in 2009, apparently. But we’ve talked about it a number of times since as it continued to develop.
Lately, though, I’m seeing more resources that are offering JBrowse in addition to their existing GBrowse installations. Increasingly the announcements are coming out that GBrowse support is ending and the move to JBrowse is underway. And sometimes people with new genomes to release are going right to JBrowse, as I noticed with this one not too long ago: YersiniaBase (http://www.ncbi.nlm.nih.gov/pubmed/25591325).
Like GBrowse, JBrowse is an open-source member of the GMOD construction set. Conveniently for me, just as I was planning this time, the developers provided a “State of the Browser, 2016” blog post that’s a great summary of “where we stand” (as some relationships are known to call it). So you can have a look at that, and check out other helpful resources like their publications and presentations.
This week, though, for our video tip we’ll have a look at the Araport video that was recently released that examines how to search JBrowse with short sequences, using their installation. If you are new to Araport, you can see a previous tip we did on the basics: Video Tip of the Week: Araport, Arabidopsis Portal. Like the other GMOD tools, a group with a given focus–in this case Arabidopsis, but it could be any species or topic–can take the basic framework for JBrowse and customize it to serve the needs of the research community. So although this is a plant genomics site, the foundations of the JBrowse software will be the same and you can expect similar features at other sites.
So start getting comfortable with JBrowse, as you’ll be seeing more and more of it as new species and research focus groups choose this as their browser. In fact, as I was preparing this tip yesterday, the new LotusBase JBrowse came along:
— LotusBase (@lotusbase) March 1, 2016
JBrowse main site: http://jbrowse.org/
Araport main site: http://www.araport.org/
Follow the official JBrowse twitter account: https://twitter.com/usejbrowse
Or JBrowseGossip: https://twitter.com/JBrowseGossip
Krishnakumar, V., Hanlon, M., Contrino, S., Ferlanti, E., Karamycheva, S., Kim, M., Rosen, B., Cheng, C., Moreira, W., Mock, S., Stubbs, J., Sullivan, J., Krampis, K., Miller, J., Micklem, G., Vaughn, M., & Town, C. (2014). Araport: the Arabidopsis Information Portal Nucleic Acids Research, 43 (D1) DOI: 10.1093/nar/gku1200
Skinner, M., Uzilov, A., Stein, L., Mungall, C., & Holmes, I. (2009). JBrowse: A next-generation genome browser Genome Research, 19 (9), 1630-1638 DOI: 10.1101/gr.094607.109