Broad's newly released Genomics Data Viewer IGV
From the Genome-Technology mailing list I found about about this software release from the Broad Institute:
Broad Institute Makes Genomics Data Viewer Public
NEW YORK (GenomeWeb News) – The Broad Institute of MIT and Harvard has created a genomics informatics tool that will allow researchers to visualize genomic information, and has made it publicly available for free, Broad said today….
So of course I went to check it out. Because I love new software! You can check it out yourself here:
Integrative Genomics Viewer: http://www.broad.mit.edu/igv/
There is a quick start introduction and a movie you can watch where someone demonstrates some clicks (no audio, or if there was I didn’t get any). A quick registration gives you access. A little java downloading and you are off to the races. There is a sample data set to get you started.
My first question was: what genomes can I see? Lo and behold–the FAQ says:
Answer: Sequence is read from the genome on a server at the Broad. For sequences to appear, you must be connected to the internet, the server must be available, and the genome that you have selected must be on the server. As of July 2008, the server provides sequence for the following genomes: hg17, hg18, mm8, and mm9.
At first I thought it was a tool to pull in your own genomes and view stuff, but it appears to rely on what’s on their server. But I haven’t dug enough yet, I’m not certain that the final answer. But if you are using one of those genomes, I could see some real utility in pulling in your data as tracks and viewing it alongside the reference sequence.
Looks nice to me. I’ll be checking it out some more and I’ll let you know what I find. Feel free to add your own reviews!
Comments
Comment from Mary
Time September 18, 2008 at 7:08 AM
Hey Jim–sounds great. We are getting a lot of questions about what to do with a genome that a research group has obtained for their own research. That’s why I focused on that aspect–it is one of our frequently-asked-of-us-questions. I’ll look for the update.
Will you email registered users with updates? That’s very handy for me. Although I’m on dozens of mailing lists, it really does get my attention on new features.
Comment from Jim Robinson
Time September 18, 2008 at 9:23 AM
Mary, yes an email update will go out to registered users when this is available. ur target for this release is October 15. If you want to email me the details of your genome(s) and the types of file(s) used to describe them we will take them into account. You can email me privately or to igv-help@broad.mit.edu.
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Comment from Jim Robinson
Time September 18, 2008 at 12:08 AM
Hi, I’m the developer of this tool and can provide some clarification re genomes. The initial version ships with some built in genomes for mouse and human. The tool can be run offline with with the genome represented by a gene track, however sequence for those genomes are only through our server. Those sequences are too large to expect users to download. We will be releasing an update in mid October that enables users to import there own genome via a fasta file.