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:
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!