Forum:Best open source genome browser in 2020
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3.3 years ago
mrmrwinter ▴ 30

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 license 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

genome-browser genomics • 4.1k views
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what, my review from 2010 isn't current enough? bah! http://jermdemo.blogspot.com/2010/08/ngs-viewers-reviewed.html

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Thanks all. I'm going with IGV

Edit: After much faffing with IGV and not being able to get the sharing functions to work, I have moved to UGENE and finding it really good.

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3.3 years ago
GenoMax 139k

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

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3.3 years ago

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. One way to think about HiGlass is like Google Maps for genomic data.

Not sure how much of the commercial Valis project is open-sourced, but I think ENCODE has used it or its commercial counterpart. It is similar to HiGlass conceptually, but has its own look and feel.

Edit, March 24 2021

Speaking of WebGL-backed 1D/2D genome browsers, Kari Lavikka will be giving a VIZBI talk later this week on his WebGL-based GenomeSpy project.

It looks very sharp and also introduces concepts in the Vega data visualization grammar. The Gehlenborg lab and collaborators in their Visual Encoding project are also working on dataviz grammars.

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We do use valis-hpgv and have forked it as the primary maintainers: https://github.com/ENCODE-DCC/valis-hpgv.

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Added edit to reference GenomeSpy project

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3.3 years ago

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

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3.2 years ago

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.

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

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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.

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3.2 years ago

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).

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