Forum: Best open source genome browser in 2020
2
gravatar for mrmrwinter
3 months ago by
mrmrwinter30
University of Hull
mrmrwinter30 wrote:

What in your opinion are the bet open source genome browsers available now?

I have used several including JBrowse, Genome Workbench, and Artemis, but find them all clunky and their GUIs dated.

Genious looks very good, but its licence requirement limits distribution of results and outputs, and is ruled out on price.

I have read reviews from several years ago, but would like to know what the community recommends.

Thanks

ADD COMMENTlink modified 12 weeks ago by Carlo Yague5.7k • written 3 months ago by mrmrwinter30
2

what, my review from 2010 isn't current enough? bah! http://jermdemo.blogspot.com/2010/08/ngs-viewers-reviewed.html

ADD REPLYlink written 3 months ago by Jeremy Leipzig19k
1

Thanks all. I'm going with IGV

ADD REPLYlink written 3 months ago by mrmrwinter30
3
gravatar for GenoMax
3 months ago by
GenoMax96k
United States
GenoMax96k wrote:

Can you clarify if you mean something else when you say genome browser? IGV or IGB are not in your list.

@dariober's ASCIIGenome: https://github.com/dariober/ASCIIGenome

ADD COMMENTlink modified 3 months ago • written 3 months ago by GenoMax96k
1
gravatar for Alex Reynolds
3 months ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

Many in the current suite of browsers make you sit and wait for data to come in and get rendered. WebGL-backed HiGlass and Valis may be contenders for where browsers are headed or need to head.

I have used HiGlass for a couple projects. It supports various dataset formats and is extensible. Not sure how much of Valis is open-sourced, but I think ENCODE has used it or its commercial counterpart.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Alex Reynolds31k
1
gravatar for lieven.sterck
3 months ago by
lieven.sterck10k
VIB, Ghent, Belgium
lieven.sterck10k wrote:

GenomeView is also free to use (not sure if completely open source) and I kinda like it, does viewing as well as editing (very little do offer the editing these days)

ADD COMMENTlink written 3 months ago by lieven.sterck10k
0
gravatar for colindaven
12 weeks ago by
colindaven2.6k
Hannover Medical School
colindaven2.6k wrote:

I'm a big fan of JBrowse. I prefer it to the likes of IGB and IGV because of the much faster loading times for big BAMs. It also allows you to structure information for users so they can explore data integration.

I haven't tried JBrowse2 yet, but its on my list and brand new in 2020.

ADD COMMENTlink written 12 weeks ago by colindaven2.6k

Can you clarify if you are referring to Jbrowse Desktop or JBrowse that requires setting up a webserver?

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by GenoMax96k

I use the server version exclusively. It's not too hard to set up and you want your software where the data lives to avoid endless unnecessary data transfers.

ADD REPLYlink written 12 weeks ago by colindaven2.6k
0
gravatar for Carlo Yague
12 weeks ago by
Carlo Yague5.7k
Canada
Carlo Yague5.7k wrote:

I always use IGV to quickly check my data locally because it is quick, it has some powerful features, and I'm used to it.

But if I need to set an online genome browser for collaborators, my preference goes to the Washu epigenome browser. It is intuitive, supports a lot of different file types, there are multiple ways to easily save sessions (through files or links or names), it has nice features (for instance split screens), and the design is minimalist by default, which save time cleaning things up (hello UCSC and your thousands vertical lines).

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by Carlo Yague5.7k
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