I love IGV!

Well sorry for the proclamation

But I think it's really nice that you have a relatively small footprint for a application that's cross platform.

anyway I needed to view a few regions of a merged bam file that's aligned to hg18 from 1000 genomes project.
You would think I might have copies of the hg18 lying around on every server so that I can just use 'samtools tview in.bam ref.fasta'

But unfortunately I don't and I am not really looking forward to downloading the hg18 just for a verification exercise.

Luckily I remembered that IGV has prebuilt human genome references that's available on the fly.
with a few clicks, I was happily viewing the regions of interest. (I downloaded the compiled binary instead of using the 'launch from browser' option but that would have been cool too)

among the list of reference human genomes avail there was actually one available for 1KG specifically. How cool is that?


Go on take the application for a run if you haven't!

http://www.broadinstitute.org/software/igv/download

What do I do with a PGM?

I am curious if 1 Gbp is enough for broad views of metagenomics, cursory glances of WGS for eukaryotes, and targetted sequence capture..  here's views by others on how they would use the PGM

IonTorrent: Benchtop Sequencing, Streamlined

from MassGenomics by Dan Koboldt

PGM Applications

It’s a good thing to see the PGM constantly evolving - first the throughput was doubled, and now sample prep time cut substantially. At the price points we’re talking about, this might easily become standard equipment or small labs, academic departments, even single investigators. The current throughput of 1 Gbp isn’t enough for whole-genome or whole-exome sequencing, but it opens the door to a number of targeted applications. In Genome Technology’s Cancer Issue this month, for example, I read about a group that’s using the PGM for a clinical test comprising 100 common mutations in human cancers.
Essentially, the niche for PGM, MiSeq, and GS Junior is everything that’s not quite enough for a full-on sequencing run. A few examples come to mind:

1. Microbial sequencing. For bite-sized genomes, 1 Gbp should be more than enough. Imagine walking into a clinic to have your strain of Streptococcus or some other infection sequenced the same day.
2. Family linkage studies. With a few family members and a reasonably-sized linkage peak, you could sequence all gene-coding exons across a region of interest, either by PCR or custom capture.
3. Orthogonal validation. Whole-genome and whole-exome studies might identify hundreds of putative mutations. Emphasis on putative. No matter how good your algorithms and filters are, there will be some false positives. Here’s an opportunity for a small, fast validation instrument. Preferably, you choose a different sequencing technology for validation (e.g. PGM for Illumina, MiSeq for SOLiD).

For more, see Keith Robison’s post at Omics! Omics! or Matthew Herber’s blog on Forbes.com.