Question: "web browser" compatible genome browsers
1
gravatar for Abhi
2.1 years ago by
Abhi1.4k
United States
Abhi1.4k wrote:

I am looking for solutions for visualizing genomics data which support viewing data on a _web browser_. I know of two possible solutions but mostl 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)

browser genome • 785 views
ADD COMMENTlink modified 4 weeks ago by dbarrios0 • written 2.1 years ago by Abhi1.4k
6
gravatar for Mary
2.1 years ago by
Mary11k
Boston MA area
Mary11k wrote:

Biodalliance: http://www.biodalliance.org/

ADD COMMENTlink written 2.1 years ago by Mary11k
3
gravatar for Alex Reynolds
2.1 years ago by
Alex Reynolds19k
Seattle, WA USA
Alex Reynolds19k wrote:

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.) "

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Alex Reynolds19k

thanks Alex. just wondering if you can also comment on their performance if you have used/implemented them locally at your workplace. It will definitely save me few hours/days.

-A

ADD REPLYlink written 2.1 years ago by Abhi1.4k
1

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.

ADD REPLYlink written 2.1 years ago by Alex Reynolds19k
3
gravatar for Juke-34
2.1 years ago by
Juke-34950
Sweden
Juke-34950 wrote:

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.

ADD COMMENTlink written 2.1 years ago by Juke-34950
1
gravatar for Evgeniia Golovina
2.1 years ago by
Russia
Evgeniia Golovina660 wrote:

List of genome browsers from Wikipedia - https://en.wikipedia.org/wiki/Genome_browser

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Evgeniia Golovina660
1
gravatar for h.mon
2.1 years ago by
h.mon6.6k
Brazil
h.mon6.6k wrote:

GBrowse fits the bill as well.

ADD COMMENTlink written 2.1 years ago by h.mon6.6k
0
gravatar for dbarrios
4 weeks ago by
dbarrios0
Spain/Salamanca/USAL
dbarrios0 wrote:

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.

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by dbarrios0
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