Search Results for: annotation

Analyzing PacBio Data with SNP & Variation Suite

         March 21, 2012

As most in the Golden Helix community are aware, SNP & Variation Suite (SVS) can handle all sorts of data including files from Affymetrix, Illumina, Agilent, and Complete Genomics with its powerful data management capabilities. Announced in February, SVS is now part of the Pacific Biosciences Partner Program and has the ability to analyze PacBio files.

Is NGS the Answer?

         November 9, 2011

While there is a lot of excitement in the industry about Next-Generation Sequencing, questions remain as to whether it will be “the answer” to the ails of the genetic research industry. I recently had the opportunity to sit down with three of Golden Helix’s thought leaders and ask a few questions about NGS – Gabe Rudy, Vice President of Product… Read more »

Wondering what SVS can do for a PhD student? Just ask Sander.

         September 14, 2011

Sander van der Laan is like many Ph.D. students in the genomic analysis space. He has a lot of data and a lot of ideas about how to analyze it. His professor wants results. He’s the only one doing genetics (everyone else in his department is doing proteomics), so there’s always too much to do. And he finds command-line tools… Read more »

Marker Map Manipulation Improvements in SVS 7.5

         August 31, 2011

Manipulating a marker map in SVS has never been easier, thanks to expanded functionality in SVS 7.5.  Have you ever wanted to view annotation data next to marker map data?  Or expand the current marker map with spreadsheet data to create a custom map?  SVS 7.5 features two new functions that can accomplish these tasks. Adding Annotation Data to a… Read more »

SVS 7.5 Now Available!

         July 28, 2011

More powerful rare variant analysis and visualization techniques We are proud to unveil SNP & Variation Suite (SVS) 7.5! The fifth installment of SVS delivers the most powerful rare variant analysis tools with the latest advances in tertiary or “sense making” methods for DNA next-gen sequencing. This release also adds some cool and productive features to our popular Genome Browser…. Read more »

Going Coast to Coast for the Latest NGS News

         June 23, 2011

Last week I was able to attend two very interesting conferences about the latest developments in the analysis of sequence data.  I started the week in San Diego at the Illumina iDEA Conference and finished it in Philadelphia at Children’s Hospital of Philadelphia’s (CHOP) Third Annual Next-Generation Sequencing Symposium.  The Illumina conference was an opportunity to learn about the latest… Read more »

A Hitchhiker’s Guide to Next Generation Sequencing – Part 2

         December 9, 2010

When you think about the cost of doing genetic research, it’s no secret that the complexity of bioinformatics has been making data analysis a larger and larger portion of the total cost of a given project or study. With next-gen sequencing data, this reality is rapidly setting in. In fact, if it hasn’t already, it’s been commonly suggested that the… Read more »

Recent Publications on Type 2 Diabetic Retinopathy, Grapevine Flavor, Pulminary Function, and Pharmacogenetics Testing

         November 30, 2010

Let’s kick off this month’s recognition with Audrey Papp and Wolfgang Sadee at Ohio State University for their work on “Flavopiridol Pharmacogenetics: Clinical and Functional Evidence for the Role of SLCO1B1/OATP1B1 in Flavopiridol Disposition” just published in PLoS ONE. (All abstracts below.) Also in pharmacogenetics (albeit in mice) this month is Tristan Sissung at the NIH National Cancer Research. His… Read more »

Conference Report: International Genetic Epidemiology Society and Genetic Analysis Workshop

         October 27, 2010

The week of October 10-16th was a busy time in our industry.  Hundreds of biostatisticians, genetic epidemiologists, and statistical geneticists gathered in Cambridge, MA for the annual conference of the International Genetic Epidemiology Society (IGES) on October 10-12, followed by the biennial Genetic Analysis Workshop (GAW) on October 13-16.  I had the opportunity to participate in both conferences, and I… Read more »

Best Practices for Incorporating Public Genotype Data in Your Study

         October 12, 2010

The Golden Helix sales team recently came to me for recommendations regarding best practices for incorporating public controls in SNP GWAS.  It seems that there has been a surge of questions regarding this practice over the past few weeks from our customers.  Initially, I laughed at the irony of being asked to outline the best practices for what I see… Read more »