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Given some genomic data in a well-known format (e.g. GFF) with gene models, what tool(s) do you use to visualize that data. What tools allow you to add your own tracks of data easily? I'm interested in both desktop and web-based tools--with preference to those that are customizable via some kind of API. |
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I like the Broad's IGV: http://www.broadinstitute.org/igv/ for genome browsing. It handles lots of common data formats, including SAM/BAM files if you're dealing with NGS-scale datasets. Apparently you can talk to it it via http, but you can't say anything very complicated: http://www.broadinstitute.org/igv/PortCommands Thanks, I finally had a chance to look at this and while you can't say much, you can say enough to load some data, then (programmatically) go to a bunch of locations and save an image. very useful.
(21 May '12, 17:00)
Customer
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The Chipster Genome Viewer is also a seemingly very competent tool, with good performance and so on, developed at CSC in Finland. (click the "Chipster Genome Viewer" in the link on the Chipster page, to start it with Java Web Start). Someone here at UPPNEX who tested it thought it was at least comparable to IGV, even though IGV still seems a more mature piece of software. Chipster is continuously being worked on though, and could be interesting to keep an eye on, I think. |
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A bit different from the linear browsers listed above is the genome visualization tool circos. It can plot a wide range of different data types onto the radially displayed chromosomes. Everything can be customized and is quite easy to use. Wonderful. I haven't gone into details. But the images are really appealing.
(21 May '12, 17:01)
Customer
Does anyone know of a circos implementation in javascript? Could b in processingjs, infovis, protovis or whatever or straight html5 canvas.
(21 May '12, 17:01)
Customer
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It's interesting to see votes for the IGV; I've looked at it only recently and it does look very promising as a desktop viewer. I'm a long-time user of the Generic Genome Browser, a Bioperl-based web application. It is extremely customizable and can act as both DAS server and client. Be prepared to spend quite a bit of time "munging" your GFF files into shape and working on the config file to get the desired results. I also like Bioperl's Bio::Graphics as a way to take simple text files (including GFF) and quickly generate very attractive plots. There's a similar, but less extensive Ruby library too. I've recently tried GenomeGraphs, an R Bioconductor package. It fetches annotations from Ensembl and plots them as tracks. It's a good way to overlay quantitative data onto genomic features: here is a sample plot. |
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I'm using the well-known UCSC Genome Browser http://genome.ucsc.edu/goldenPath/help/customTrack.html I also wrote an experimental implementation of Jan Aerts' LocusTree based on BerkeleyDB (see http://plindenbaum.blogspot.com/2009/11/java-implementation-of-jan-aerts.html ) |
