easy-to-use, fast genome browser ?
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10 months ago
jerry ▴ 110

Is there an easy-to-use, fast genome browser yet? I have used IGV, and it is painfully slow when trying to load and browse a 50GB whole-genome BAM file. Also, it's not so easy to set up on a remote server for general use. Same thing for UCSC - slow, not easy to set up for general use.

Any other recommendations? Thanks!

genome browser bioinformatics • 594 views
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10 months ago
Juke34 ★ 6.4k

Here Which genome browser to use for my data? I mention a nice ressource reviewing genome browsers. But they didn't look at HiGlass ...

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10 months ago

Is there an easy-to-use, fast genome browser yet?

It all depends on what you want to do and what you expect in terms of speed and ease of use. But I doubt there can be a genome browser that is going to be as fast as, say, scrolling a text file in a text editor. When you zoom-in/out, move region, etc the browser has to do quite a bit of computation, possibly a lot of it!

browse a 50GB whole-genome BAM file

The size of the bam file in itself does not mean much. If you want to visualise small regions of a few kb or less and coverage is not crazy high, than something like IGV should be pretty quick. If you want to visualise larger regions like big chunks of chromosomes, then BAM files are going to be slow and you may need to use bigwig files instead.

Any other recommendations?

I'm happy with the browser I wrote, ASCIIGenome, because the files I work with are on a remote server and anything with GUI is, as you say, painfully slow and moving them locally is equally a pain. Loading a bam file is just:

ASCIIGenome aln.bam

If you want raw speed, samtools tview is probably by far the fastest but it's very limited in what you can do.

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A command-line genome browser - wonderful idea and impressive, I will try it out! Yeah, the "pain" is trying to interface with a GUI on a remote server. For now, everyone on the team is just downloading BAM files and installing IGV on their own laptops. But this may be a quick-to-use solution on our remote server - thanks!

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jerry : Not ideal but there is also this possibility: IGV over SSH?

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10 months ago

The lead developer behind HiGlass recently released a plugin called higlass-pileup that supports rendering BAM pileup tracks.

HiGlass does for genomic data what Google Maps and similar do for geographic data. You can zoom in and out and get different, scaled presentations of the data much more quickly than with conventional tools like UCSC, WashU or IGV browsers, which can take a bit of time to calculate what you see.

The higlass-manage tool is probably the easiest way to get a HiGlass server going.

An option similar to HiGlass might be Valis, but I haven't had much chance to set it up and kick the tires. Might also be worth taking a look at, though.

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10 months ago
steve ★ 3.0k

If you can narrow your search down to a list of genomic regions, I find it easier to use something like IGV Reports; https://github.com/igvteam/igv-reports

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10 months ago
the_dummy ▴ 30

I like Tablet genome browser.

Give it a shot...

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