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
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
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
Seeker seems like a nice HTML5 option:
I wrote that while back. Now looking at it again, the instructions seems kinda hard to understand....
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what's your input ? a genbank accession ?
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?
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
A nice, extensible starting point. Lovely, thanks for sharing.