PolITiGenomics

What’s in an Illumina GA run directory?

Wednesday, October 28th, 2009 Posted in genomics, IT | No Comments »

One of the main things that differentiates genomics from other endeavors that use a lot of disk space is that genomics file systems tend to have a lot of files ... Read more..

More than cells, more than bytes

Friday, October 23rd, 2009 Posted in genomics, IT | 4 Comments »

In a recent New York Times article, Jimmy Lin from of the University of Maryland is quoted as saying, "Science these days has basically turned into a data-management problem." If ... Read more..

Next-Generation Sequencing Informatics table update

Monday, October 5th, 2009 Posted in genomics, IT | 2 Comments »

I have made some updates to the Next-Generation Sequencing Informatics table. Specifically, I have updated the numbers for 454 Ti, including paired-end information, and added information on the Illumina GA ... Read more..

Breakin’ 3: Genomic Variations

Friday, October 2nd, 2009 Posted in genomics | No Comments »

In the long awaited follow up to Breakin' and Breakin' 2, Ken Chen has released BreakDancer. As described in his Nature Methods article and a recent Genome Technology article, BreakDancer ... Read more..

My secret past

Wednesday, September 16th, 2009 Posted in genomics, IT | No Comments »

Now everyone will know about my secret past before I joined The Genome Center: David Dooling: Gangbusters at the Genome Center. Bio-IT World also has a nice interview with Clive ... Read more..

SNP vs. SNP

Friday, July 17th, 2009 Posted in genomics | 7 Comments »

At the NHGRI Sequencing Advisory Panel meeting last week, there was some confusion about how we use SNP array data and dbSNP in the DNA sequencing world. SNP arrays are, ... Read more..

Download sequence data fast

Thursday, July 16th, 2009 Posted in genomics, IT | No Comments »

More and more data are being submitted to the NCBI Short Read Archive (SRA). So you may ask yourself, "How am I going to download all that data?" Well, as ... Read more..

Cancer Genomics Tools

Wednesday, July 15th, 2009 Posted in genomics | No Comments »

The folks in our Medical Genomics group have compiled a list of bioinformatics tools that are useful in the field of cancer genomics. The tools, mostly focused on next/second-generation sequence ... Read more..

OSCON lead up

Monday, July 13th, 2009 Posted in genomics, IT | No Comments »

Last week I did an interview with James Turner at O'Reilly about my upcoming talk at OSCON. It turns out that James is a bit of a genomics nut and ... Read more..

VarScan published

Tuesday, June 23rd, 2009 Posted in genomics | No Comments »

VarScan, a tool developed at The Genome Center to detect variants in massively parallel sequence data has been published in Bioinformatics. VarScan can process both 454 and Solexa data of ... Read more..