GMOD/jbrowse — Issue #5: Make browser usable for large next-generation assemblies.
Author: jbrowsetix
Created: 2012-01-25 19:37:39+00:00
State: open
Labels: from-lighthouse, |S| new

Hello,
I have a few genome assemblies in progress (in the 2-3Gb range). This tool would be great but since these assemblies are highly fragmented (usually 150k to 300k scaffolds not assigned to any higher level group like a chromosome) the browser fails to load. Simply running `ls` on the ./data/seq directory takes about a minute, and the ./data/refSeqs.js file is 27Mb. This is actually for one of our better assemblies. These types of genomes work fine in browsers like the UCSC genome browser since everything is stored and accessed in a mysql database. Although that is not your model, would there be an alternative, such as making a multi-level directory tree for the scaffolds, and possibly indexing the list of names so that they work reasonably fast?

Anyway I hate having to reload my assemblies into the UCSC genome browser since I am in rapid assembly and re-assembly mode. I would really like a quick light-weight program to view my assemblies in progress, visualize alignments, etc, and this tool seems like it should fit that bill really well. This program seems like it could be a perfect tool for de-novo genome assembly projects which are becoming rapidly more common. A quick, light-weight, server hosted browser like this would be great for this purpose.

Thanks for your time and consideration,
John

[original LH ticket](http://jbrowse.lighthouseapp.com/projects/23792/tickets/83)

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