PolITiGenomics

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..

Illumina cluster needs

Thursday, June 18th, 2009 Posted in genomics, IT | No Comments »

There is an interesting thread over at the Solexa Google Group about the IT infrastructure needed to support an Illumina Genome Analyzer (GA). The discussion focuses mostly on the cluster ... Read more..

Sequencing AML with paired-end reads

Wednesday, April 29th, 2009 Posted in genomics | No Comments »

When The Genome Center performed the sequencing of the first whole cancer genome, the state of the art for next-generation sequencing was single-end, or fragment, reads. While these data allowed ... Read more..

Sequencing — the past, present, and future

Tuesday, April 21st, 2009 Posted in genomics | No Comments »

Science Magazine has a nice article, Sanger Who? Sequencing the Next Generation, describing past sequencing technology, the current "next-generation" sequencing instruments and their capabilities, and several of the companies working ... Read more..

The ls in lsgmake-gap

Friday, April 3rd, 2009 Posted in genomics, IT | No Comments »

I have released a new version of lsgmake-gap, 0.13 (md5). This version puts the "ls" back in lsgmake-gap by adding the --bsub-options command-line option which allows the user to specify ... Read more..

lsgmake-gap for GAPipeline-1.3

Wednesday, February 25th, 2009 Posted in genomics, IT | 2 Comments »

I have just posted the latest version of lsgmake-gap, 0.12 (md5). This version of lsgmake-gap supports the additional Bustard targets introduced in GAPipeline-1.3 (it should still work with earlier versions ... Read more..

My talk at AGBT

Wednesday, February 18th, 2009 Posted in genomics | 4 Comments »

Several people have asked me to post my slides from AGBT. Given the type of slides I prepare, I thought that might be less than useful, so I recorded my ... Read more..

The scale up

Friday, February 6th, 2009 Posted in genomics, IT | 5 Comments »

It was announced this morning that we will be getting 21 more Illumina GA2 instruments, bringing our total to 35 at The Genome Center. No doubt it will be a ... Read more..

Elaine Mardis on Cancer in Technology Review

Wednesday, December 24th, 2008 Posted in genomics | No Comments »

Elaine Mardis, Co-Director of The Genome Center has a brief article in the January/February 2009 issue of Technology Review discussing the application of next-generation sequencing technologies to cancer research entitled ... Read more..

AML at ASH

Wednesday, December 10th, 2008 Posted in genomics | No Comments »

It seems the publication of the first whole cancer genome sequence is getting a good reception in hematology circles. This past Saturday at the 50th Annual Meeting of the American ... Read more..