What are the best genomic data visualisation tools and APIs (in 2015)?

Question

[bedeabc]

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 (What Tools/Libraries Do You Use To Visualize Genomic Feature Data?), 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

[Pierre Lindenbaum]

what's your input ? a genbank accession ?

[bedeabc]

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?

[Pierre Lindenbaum]

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

[bedeabc]

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

Answer 1

[bedeabc]

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

Answer 2

[bedeabc]

Seeker seems like a nice HTML5 option:

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

[Damian Kao]

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

[skbrimer]

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