Question: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
47
gravatar for brentp
4.1 years ago by
brentp17k
Denver, Colorado
brentp17k wrote:

Given some genomic data in a well-known format (e.g. GFF) with gene models, what tool(s) do you use to visualize that data. What tools allow you to add your own tracks of data easily? I'm interested in both desktop and web-based tools--with preference to those that are customizable via some kind of API.

ADD COMMENTlink modified 13 months ago by Victor Lyuboslavsky120 • written 4.1 years ago by brentp17k
22
gravatar for Cassj
4.1 years ago by
Cassj1.1k
London
Cassj1.1k wrote:

I like the Broad's IGV: http://www.broadinstitute.org/igv/ for genome browsing. It handles lots of common data formats, including SAM/BAM files if you're dealing with NGS-scale datasets. Apparently you can talk to it it via http, but you can't say anything very complicated: http://www.broadinstitute.org/igv/PortCommands

ADD COMMENTlink written 4.1 years ago by Cassj1.1k

Thanks, I finally had a chance to look at this and while you can't say much, you can say enough to load some data, then (programmatically) go to a bunch of locations and save an image. very useful.

ADD REPLYlink written 2.9 years ago by brentp17k
17
gravatar for Allpowerde
4.1 years ago by
Allpowerde1.1k
Allpowerde1.1k wrote:

A bit different from the linear browsers listed above is the genome visualization tool circos. It can plot a wide range of different data types onto the radially displayed chromosomes. Everything can be customized and is quite easy to use.

alt text

ADD COMMENTlink written 4.1 years ago by Allpowerde1.1k

Wonderful. I haven't gone into details. But the images are really appealing.

ADD REPLYlink written 3.0 years ago by Dejian890

Does anyone know of a circos implementation in javascript? Could b in processingjs, infovis, protovis or whatever or straight html5 canvas.

ADD REPLYlink written 2.8 years ago by Petervermont0
15
gravatar for Neilfws
4.1 years ago by
Neilfws41k
Sydney, Australia
Neilfws41k wrote:

It's interesting to see votes for the IGV; I've looked at it only recently and it does look very promising as a desktop viewer.

I'm a long-time user of the Generic Genome Browser, a Bioperl-based web application. It is extremely customizable and can act as both DAS server and client. Be prepared to spend quite a bit of time "munging" your GFF files into shape and working on the config file to get the desired results.

I also like Bioperl's Bio::Graphics as a way to take simple text files (including GFF) and quickly generate very attractive plots. There's a similar, but less extensive Ruby library too.

I've recently tried GenomeGraphs, an R Bioconductor package. It fetches annotations from Ensembl and plots them as tracks. It's a good way to overlay quantitative data onto genomic features: here is a sample plot.

ADD COMMENTlink written 4.1 years ago by Neilfws41k
15
gravatar for Andrew Su
4.0 years ago by
Andrew Su4.0k
San Diego, CA
Andrew Su4.0k wrote:

Late to the party here, but jbrowse has a nice ajaxy interface...

ADD COMMENTlink written 4.0 years ago by Andrew Su4.0k
1

Jbrowse is not just a pretty face - the feature encoding is JSON NClist which should scale well. Shame they are using the bioperl GFF3 parser really.

ADD REPLYlink written 4.0 years ago by Casbon2.7k
1

Casbon, what parser would you use instead?

ADD REPLYlink written 3.2 years ago by Ihh20

something that doesnt use so much memory ;)

ADD REPLYlink written 3.1 years ago by Casbon2.7k

JBrowse's way of getting data into the browser is...special. Our group started with JBrowse to write a platform for our users here, and ended up rewriting large hunks of it, and basically throwing out its backend and replacing it.

ADD REPLYlink written 3.1 years ago by User 5267100
14
gravatar for Pierre Lindenbaum
4.1 years ago by
France
Pierre Lindenbaum58k wrote:

I'm using the well-known UCSC Genome Browser http://genome.ucsc.edu/goldenPath/help/customTrack.html

I also wrote an experimental implementation of Jan Aerts' LocusTree based on BerkeleyDB (see http://plindenbaum.blogspot.com/2009/11/java-implementation-of-jan-aerts.html )

LocusTree

ADD COMMENTlink written 4.1 years ago by Pierre Lindenbaum58k
1

Just to chip in my first comment on BioStar. I also use Gbrowse for this job. Hugely configurable and very easy to install and add tracks to.

I've recently been using Gbrowse2, which is a pretty slick improvement. A comprehensive install guide is available at the GMOD website http://gmod.org/wiki/GBrowse_2.0_HOWTO

ADD REPLYlink written 4.1 years ago by Ian Simpson860
14
gravatar for Dave Clements
3.2 years ago by
Dave Clements540
Dave Clements540 wrote:

There's was a great review paper on genome visualization in Nature Methods last year: Visualizing genomes: techniques and challenges, by CB Nielsen, et al. It's part of a whole supplement on visualizing biological data.

And, for what it's worth, both GBrowse and JBrowse are both highly configurable and built to be installed locally, and have active communities supporting them.

ADD COMMENTlink written 3.2 years ago by Dave Clements540
13
gravatar for brentp
4.1 years ago by
brentp17k
Denver, Colorado
brentp17k wrote:

thanks for all the replies so far. i just want to add a couple i've found: Annoj with a nice demo here: http://neomorph.salk.edu/epigenome/epigenome.html seems to be a pretty nice web-interface and i've been able to get my own annotations drawn. it may be an abandoned project, and i wasn't able to find the javascript source (only the packed/minified version).

also genometools wraps cairo to allow simple drawing of regions: here's the image from their home page. alt text And they have bindings to a variety of scripting languages.

ADD COMMENTlink written 4.1 years ago by brentp17k

Anno-j has a really nice architecture. I used it to setup an Arabidopsis browser for custom experimental data along with their existing tracks: http://arab-annoj.appspot.com/ The downside is that I haven't seen any active development in a while, which is a shame.

ADD REPLYlink written 4.0 years ago by Brad Chapman8.1k

I thought I had posted GenomeTools as a response to this question. Maybe it was a similar question. Anyway, I'm a happy "customer"--very pleased with their web interface and local application. I haven't tapped into their APIs yet though...

ADD REPLYlink written 3.4 years ago by Daniel Standage3.0k
9
gravatar for Pierre Lindenbaum
3.5 years ago by
France
Pierre Lindenbaum58k wrote:

Another one I found today: GView: https://www.gview.ca/wiki/GView/WebHome

GView is a java package used to display and navigate bacterial genomes. GView is useful for producing high-quality genome maps for use in publications and websites, or used as a visualization tool in a sequence annotation pipeline. Users can interact with the genome using a powerful pan-and-zoom interface, or GView can write static images of a genome to a file. GView can draw a genome using either circular or linear layouts, with additional layout types planned for future release.

alt text

ADD COMMENTlink modified 15 months ago • written 3.5 years ago by Pierre Lindenbaum58k
1

thanks, that's useful.

ADD REPLYlink written 3.5 years ago by brentp17k
8
gravatar for Istvan Albert
4.1 years ago by
Istvan Albert ♦♦ 39k
University Park, USA
Istvan Albert ♦♦ 39k wrote:

For desktop level genome visualization the Integrated Genome Browser is a very nice tool.

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Istvan Albert ♦♦ 39k
8
gravatar for Stew
4.0 years ago by
Stew1.1k
Cambridge
Stew1.1k wrote:

I would vote for IGB (Integrated Genome Browser). It can handle a large number of tracks and large genome scale data sets. It is highly configurable and very fast. You can also talk to it via some ports . I sometimes generate excel files with hyperlinks that make IGB jump to specific locations, which can be really useful. So you can have an excel sheet with a list of genes which you can click in one window and IGB jumps to that gene.

Another great feature is the ability to do data manipulation, such as merging tracks using logic, to get overlapping or unique features. You can also do things like log2 transformations.

ADD COMMENTlink written 4.0 years ago by Stew1.1k
8
gravatar for Chase Miller
3.2 years ago by
Chase Miller370
Boston College
Chase Miller370 wrote:

Scribl is based on HTML5 Canvas which allows for some nice interactivity (demo). Though it is a little light on features.

ADD COMMENTlink written 3.2 years ago by Chase Miller370

this doesn't seem to work with firefox

ADD REPLYlink written 3.2 years ago by Michael Dondrup27k

Fixed now for firefox. Although the performance is better in chrome/safari

ADD REPLYlink written 3.2 years ago by Chase Miller370
7
gravatar for Chris Miller
4.1 years ago by
Chris Miller12k
St. Louis, MO
Chris Miller12k wrote:

I'll put in a plug for Genboree, which my lab develops. It's essentially a genome browser with personalized databases/wikis, access control, and integration with Galaxy. It can import UCSC tracks and you can add any data that maps to genomic coordinates. It also has a REST API that's fairly new.

Since I do a lot of copy-number work, I also do quite a bit of sanity-check visualization with R, often just using simple tweaks of the plot command, but sometimes pulling in packages to help.

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Chris Miller12k
7
gravatar for Nicojo
4.1 years ago by
Nicojo1.0k
Kyoto, Japan
Nicojo1.0k wrote:

I use Artemis and ACT from the Sanger Institute. The former is a genome viewer and annotation tool. The latter is used for comparing genomes.

However, I'm not sure that there's an API for it...

ADD COMMENTlink written 4.1 years ago by Nicojo1.0k
6
gravatar for Paulo Nuin
4.0 years ago by
Paulo Nuin3.5k
Canada
Paulo Nuin3.5k wrote:

Circos would get my vote too.

ADD COMMENTlink written 4.0 years ago by Paulo Nuin3.5k

http://circos.ca/software/download/

ADD REPLYlink written 2.1 years ago by Malachi Griffith6.6k
6
gravatar for Rm
3.4 years ago by
Rm6.5k
US
Rm6.5k wrote:

Broad Institute's Integrative Genomics Viewer (IGV) will be my first choice, some other tools also to look at..

mVISTA software: Genome Alignment (AVID) and visualization (VISTA) programs.

VISTA whole-genome pipeline software

GeneViTo is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction.

BioViews: Java-Based Tools for Genomic Data Visualization

GenomePixelizer - Genome Visualization Tool: GenomePixelizer-a visualization program for comparative genomics within and between species

SilverGene & SilverMap are useful to look at blast results of a gene mapped to a genome.

ADD COMMENTlink written 3.4 years ago by Rm6.5k
5
gravatar for Ann Loraine
3.2 years ago by
Ann Loraine50
Ann Loraine50 wrote:

For visualization of genome re-arrangements, take a look at Gremlin. The authors compared it to Circos and found that Gremlin led to more and deeper insights for users than Circos. See: http://vis.cs.brown.edu/docs/pdf/g/OBrien-2010-GIV.pdf.html.

ADD COMMENTlink written 3.2 years ago by Ann Loraine50

Unfortunately it seems that this software is not yet available for download according to Ben Raphael's lab software page: http://compbio.cs.brown.edu/software.html

ADD REPLYlink written 2.1 years ago by Malachi Griffith6.6k
4
gravatar for Giulietta - Ensembl Helpdesk
3.2 years ago by
Cambridge, UK

Wow, there are lots of options to do this! One that hasn't been mentioned is the Ensembl Genome Browser. The positive would be the ability to compare your gene models to Ensembl annotation along the genome. For example, in this view:

http://www.ensembl.org/Homo_sapiens/Location/View?r=6:133017695-133161157

Click 'Manage your data' at the left. Either upload a GFF file to Ensembl using the 'Upload data' option at the left of the menu, or use 'Attach URL' to attach your file without uploading it to Ensembl. In both cases, you will be able to view your gene models along the genome, and turn on or off other data tracks.

If you need any help with this option, give it a try or ask our helpdesk to guide you. helpdesk[?]ensembl.org

ADD COMMENTlink written 3.2 years ago by Giulietta - Ensembl Helpdesk980
4
gravatar for Casbon
3.1 years ago by
Casbon2.7k
Casbon2.7k wrote:

Dalliance is looking nice: http://www.biodalliance.org/

ADD COMMENTlink written 3.1 years ago by Casbon2.7k
4
gravatar for Khader Shameer
3.0 years ago by
Rochester, MN
Khader Shameer14k wrote:

I am currently using LocusZoom for annotation of our GWAS data. It provides neat way to visualize crowded locus regions.

ADD COMMENTlink written 3.0 years ago by Khader Shameer14k

thanks, i have something i can send to that right now.

ADD REPLYlink written 3.0 years ago by brentp17k
4
gravatar for Pierre Lindenbaum
15 months ago by
France
Pierre Lindenbaum58k wrote:

One more (January 2013): ChromoZoom

ChromoZoom: a flexible, fluid, web-based genome browser

Bioinformatics (2012)

doi: 10.1093/bioinformatics/bts695

enter image description here

ADD COMMENTlink written 15 months ago by Pierre Lindenbaum58k
3
gravatar for Puthier
3.5 years ago by
Puthier240
Puthier240 wrote:

MagicViewer seems also to be a nice solution.

ADD COMMENTlink written 3.5 years ago by Puthier240
3
gravatar for Pawel Szczesny
3.4 years ago by
Pawel Szczesny2.6k
Poland
Pawel Szczesny2.6k wrote:

I like Argo from Broad Institute much more than IGV. It works well for visualizing and manually annotating whole genomes and it's reasonably fast. It can run standalone or as an applet/webstart (it's written in Java and distributed as a single jar file).

ADD COMMENTlink written 3.4 years ago by Pawel Szczesny2.6k
3
gravatar for Chris Whelan
3.2 years ago by
Chris Whelan470
Portland, OR
Chris Whelan470 wrote:

I'll throw another name into the ring - I've recently been using SeqMonk for some of this type of stuff: http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/README.txt. I like its capabilities for doing quantitation over user-defined probes along your genome. There's lots of flexibility there for starting an exploratory enrichment-type analysis of your data.

ADD COMMENTlink written 3.2 years ago by Chris Whelan470
3
gravatar for Pierre Lindenbaum
2.1 years ago by
France
Pierre Lindenbaum58k wrote:

One more from VizBi 2012: Chipster http://chipster.csc.fi/

alt text

ADD COMMENTlink written 2.1 years ago by Pierre Lindenbaum58k
2
gravatar for ALchEmiXt
2.1 years ago by
ALchEmiXt1.4k
(close to) Lelystad, The Netherlands
ALchEmiXt1.4k wrote:

Very late to join the party but here is an example of an API only viewer in R;

It is called genoplotR and its production/publication ready graphics can be generated within R. It is highly tunable.

Just a random example below;

alt text

ADD COMMENTlink written 2.1 years ago by ALchEmiXt1.4k
2
gravatar for Pierre Lindenbaum
21 months ago by
France
Pierre Lindenbaum58k wrote:

One more via: https://twitter.com/klmr/status/227780333981028352

http://www.genomemaps.org/

ADD COMMENTlink written 21 months ago by Pierre Lindenbaum58k
2
gravatar for Irsan
18 months ago by
Irsan3.5k
Amsterdam
Irsan3.5k wrote:

Also see the post about Drawing Chromosome Ideogams With Data

ADD COMMENTlink modified 18 months ago • written 18 months ago by Irsan3.5k
2
gravatar for Victor Lyuboslavsky
13 months ago by
Austin, TX, United States
Victor Lyuboslavsky120 wrote:

GenomeBrowse from Golden Helix is a desktop client.

ADD COMMENTlink written 13 months ago by Victor Lyuboslavsky120
1
gravatar for Anuraj Nayarisseri
2.6 years ago by
Indore
Anuraj Nayarisseri620 wrote:

There is one tool called Artemis which is developed by Sanger institute.

http://www.sanger.ac.uk/resources/software/artemis/

and one more tools called SeqVista

http://zlab.bu.edu/SeqVISTA/

Hope this will help you.

ADD COMMENTlink written 2.6 years ago by Anuraj Nayarisseri620
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