I am looking for solutions for visualizing genomics data which support viewing data on a web browser. I know of two possible solutions but mostly likely I am missing few.
Key requirements
The solution should be able to integrate into a browser and not a standalone solutions like IGV which are great but not applicable for our use case.
Also if you guys can summarize your experience on using the browsers you recommend, in terms of scalability, data integration capabilities etc.
Thanks!
-Abhi
edit: corrected GA browse link (h.mon)
7 answers
Biodalliance: http://www.biodalliance.org/
- UCSC Genome Browser (and the more self-contained Genome Browser in a Box)
- WashU Epigenome Browser
- Genome Maps
- Annmap
For performance, the lead WashU browser developer offered some advice on the basis on his lab's setup here: https://plus.google.com/115377858150593521942/posts/UsbKAJuqEVC
[O]ne of our public server used a Dell M620 server, which has 24-core CPU, 128G memory, 2-300G Raid1 disk for operating system, tracks are then hosted on a NFS for sharing between servers. (Tracks could host on same or different servers as long as you have a URL for each track.)
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Alex Reynolds
I find web-based genome browsers to work reasonably well when the underlying backend system is adequately powered. Running a browser and its database on a VM, for instance, might offer some maintenance benefits for the IT manager, but it will really hurt performance for the end user. You want to run these on real hardware, with sufficient memory and disk space.
JBrowse is a good choice. I'm using WebApollo (http://genomearchitect.org/) which is based on JBrowse and it works perfectly well. It's fast even with huge annotation files. I like the fact that it's open source and part on the GMOD project (http://gmod.org/wiki/Main_Page). The developer team is really efficient and reachable.
List of genome browsers from Wikipedia - https://en.wikipedia.org/wiki/Genome_browser
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Evgeniia Golovina
I'd say the fastest and the most memory-efficient genome browser is Persephone. They have a commercial Windows version for corporations but recently they released a free web-based browser. It shows multiple chromosomes together, allows to compare them and the speed is fantastic. It sits on top of a database (MySql or Oracle) with public data but AFAIK they will allow to overlay your own data. Check it out: http://web.persephonesoft.com
Another option is D3 Genome Browser (d3gb.usal.es). It is a multi-platform software for quick and in-browser visualization of genomic data and it is available as an R package, a Python module and a WordPress plugin.
It supports the most popular genomic formats as input, the output is a web page with vector graphics and it can be executed as a local file in a Browser or shared with an application Web server.
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