Question: Other Genomic Viewer Like Igv
2
gravatar for marcodpc
5.9 years ago by
marcodpc30
marcodpc30 wrote:

Are there other genomic viewer like IGV ?

viewer genomic igv • 11k views
ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 5.9 years ago by marcodpc30
4
gravatar for Obi Griffith
5.9 years ago by
Obi Griffith17k
Washington University, St Louis, USA
Obi Griffith17k wrote:

I think the most similar and closest competitor is the Savant Genome Browser. Like IGV, it is a stand-alone, java-based application which allows you to quickly upload and visualize NGS data (e.g. bam files) in the context of a reference genome, annotation tracks, custom bed files etc. It has a number of different visualizations and plugins which distinguish it from IGV. But, in general they are quite similar. If you've used IGV then Savant will be fairly intuitive and the choice between them is somewhat subjective. My impression is that development of Savant is maybe a little bit more open and community-driven than IGV. The Savant paper from summer 2012 gives a good overview. Which Multiscale Genome Browser Is The Best At Visualizing Structural Variants? compares Savant and IGV in the context of visualizing structural variants.

ADD COMMENTlink written 5.9 years ago by Obi Griffith17k

is IGV the most used ? I try to use Savant... but it isn't so intuitive... I read biostar post with compares, but I need to justify the use of IGV...

ADD REPLYlink written 5.9 years ago by marcodpc30
2
gravatar for Jelena Aleksic
5.9 years ago by
Cambridge, UK
Jelena Aleksic900 wrote:

I used to use IGB (http://bioviz.org/igb/) for visualising things like bed files. I think it's pretty. I switched to IGV since I started working mainly with NGS data though, as it's the one everyone recommended. Haven't tested whether and how well IGB can deal with it. Uploading custom tracks to UCSC also actually works pretty nicely, particularly since it gives you so much other data you can visualise alongside your own.

ADD COMMENTlink written 5.9 years ago by Jelena Aleksic900
2
gravatar for Ido Tamir
5.9 years ago by
Ido Tamir5.0k
Austria
Ido Tamir5.0k wrote:

"like" in which way? client side, java, reliable, non-crashing, low on memory requirements, fast, digesting many file formats, usable UI etc..

Genome browsers there are a lot. Really usable ones, not so many. http://en.wikipedia.org/wiki/Genome_browser

and this list is not even complete with eg chipmonk missing.

ADD COMMENTlink written 5.9 years ago by Ido Tamir5.0k

Added Chipmonk :)

ADD REPLYlink written 5.9 years ago by Jelena Aleksic900

"like" in which way? - exactly right.

ADD REPLYlink written 5.9 years ago by Neilfws48k

I mean "like" as: client side, java, non-crashing but also intuitive, usable, reliable.

ADD REPLYlink written 5.9 years ago by marcodpc30
1
gravatar for Samuel Lampa
5.9 years ago by
Samuel Lampa1.2k
Stockholm
Samuel Lampa1.2k wrote:

Finnish super computing center CSC is developing a qutie powerful one, "Chipster Genome Browser", available here (you can webstart it from the link on the page). It is also written in Java, just like IGV.

ADD COMMENTlink written 5.9 years ago by Samuel Lampa1.2k
1
gravatar for bioinfo
5.9 years ago by
bioinfo690
EU
bioinfo690 wrote:

I usually use artemis for visualizing NGS data. Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. http://www.sanger.ac.uk/resources/software/artemis/

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by bioinfo690
1
gravatar for Manu Prestat
5.9 years ago by
Manu Prestat3.9k
Marseille, France
Manu Prestat3.9k wrote:

A good review about that by Jeremy Leipzig (found in that post: A: Any good BAM and SAM viewer? )

ADD COMMENTlink written 5.9 years ago by Manu Prestat3.9k
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