Other Genomic Viewer Like Igv
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8.4 years ago
marcodpc ▴ 40

Are there other genomic viewer like IGV ?

igv genomic viewer • 15k views
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8.4 years ago

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.

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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...

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8.4 years ago

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.

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8.4 years ago
Ido Tamir 5.2k

"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.

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Added Chipmonk :)

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"like" in which way? - exactly right.

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

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21 months ago
cmdcolin ★ 1.7k

I started a large list of genome browsers and general genome data viz software here https://github.com/cmdcolin/awesome-genome-visualization/

Includes mostly genome browser type things but some others (dotplots, msa, etc)

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Thanks for sharing, I find this is incredibly useful, and even more so your companion site!

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8.4 years ago
Samuel Lampa ★ 1.3k

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.

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8.4 years ago
bioinfo ▴ 800

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/

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8.4 years ago

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

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