What are the best genomic data visualisation tools and APIs (in 2015)?
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6.1 years ago
bedeabc ▴ 110

I'm looking at libraries for dynamically visualising simple custom genomic track data (references, contigs, CDSs etc), most likely for display within web pages, meaning I could use anything from static raster images to vectors or HTML5 canvas.

There are lots of options out there, and seeing as what appears to be the last good post on this issue is rather old (https://www.biostars.org/p/363/), I thought I might be useful to collate some of the approaches in use today. I'm especially interested in lightweight libraries and remote web services.

 

Some options I've found

GenomeTools: http://genometools.org/

Scribl (HTML5): http://chmille4.github.io/Scribl/

Sushi (R): https://www.bioconductor.org/packages/release/bioc/vignettes/Sushi/inst/doc/Sushi.pdf

GenoPlotR (R): http://genoplotr.r-forge.r-project.org/

GGBio (R)

Circos

 

However, my current requirements are very basic, and a simpler and lower level the library might well suffice. I just want to be able to automatically generate visualisations of small viral genome components. For example:

 

Thanks,

Bede

visualisation • 1.8k views
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what's your input ? a genbank accession ?

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Thanks Pierre. I don't mind as I haven't yet written the code to generate the coordinate data from my pipeline. I suppose GBK or GFF would seem appropriate, but I just need to supply coordinates for contigs and some labels. Does anything spring to mind?

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for genbank I wrote a xslt stylesheet converting an entry to SVG: https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/ncbi/gb2svg.xsl

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A nice, extensible starting point. Lovely, thanks for sharing.

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6.0 years ago
bedeabc ▴ 110

Another self answer.... This is the most promising I've found so far. Seems actively maintained. The required input format will be a headache for some, but is at least very transparent

Islandplot: https://github.com/lairdm/islandplot

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6.1 years ago
bedeabc ▴ 110

Seeker seems like a nice HTML5 option:

http://www.nextgenetics.net/tools/anno_view/annotator.html

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I wrote that while back. Now looking at it again, the instructions seems kinda hard to understand....

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I just looked at the examples and I can not stop laughing about the gene names. My personal favorite is turtle power.

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