Category Archives: Technology review

Is Free Software Really Free?

         May 23, 2012

The prevalence of open-source bioinformatic tools in the genetic research space is enormous. According to The North Shore LIJ Research Institute, there are over 500 genetic analysis software packages – the great majority of which are free – as of August 2010. Open-source tools are incredibly important in genetics. They allow new methodologies to be created and expanded. They tie… Read more »

DNA Variant Analysis of Complete Genomics’ Next-Generation Sequencing Data

         August 17, 2011

As I’ve mentioned in previous blog posts, one of the great aspects of our scientific community is the sharing of public data. With a mission of providing powerful and accurate tools to researchers, we at at Golden Helix especially appreciate the value of having rich and extensive public data to test and calibrate those tools. Public data allow us to… Read more »

SVS 7.5 Feature Sneak Peek: Grouping and Filtering in the Genome Browser

         June 8, 2011

Ever since the release of SNP & Variation Suite (SVS) 7.4 back in January, our software engineers have been hard at work developing new functionality for the next version, to enable researchers to have even more control over their data. (Okay, well really, they started working on it before 7.4 even came out.) While the full details of 7.5 are… Read more »

NGS Tools and Formats for Secondary Analysis: A Primer

         April 20, 2011

In a series of previous blog posts, I gave an overview of Next Generation Sequencing trends and technologies. In Part Two of the three part series, the range of steps and programs used in the bioinfomatics of NGS data was defined as primary, secondary and tertiary analysis. In Part Three I went into more details on the needs and workflows… Read more »

I Want a GPU for Computational Analysis! Which One Should I Get?

         April 14, 2011

A GPU can produce an enormous boost in performance for many scientific computing applications. Since we announced the availability of SNP & Variation Suite’s incorporation of GPUs to dramatically speed up copy number segmentation, we’ve received numerous inquiries on recommendations for what GPU to purchase. Unfortunately the technical terminology and choices can be a bit confusing. In this article I… Read more »

Updates to CNAM Make SVS the Fastest and Most Accurate Copy Number Tool for Common and Rare CNVs

         March 16, 2011

A recent email from a user of SVS: “Your CNAM Optimal Segmentation algorithm is by far the best I ever used and believe me, I’ve tried many. Great use of the GPU for segmentation – it is 3x faster than using my 8 CPUs alone and 25x faster compared to 1 CPU.” SNP & Variation Suite (SVS) version 7.4 introduced… Read more »

Checking Relatedness and/or Inbreeding in Samples as a Quality Assurance Measure

         February 10, 2011
James' whiteboard with IBD calculations

Almost every statistic that is used for significance testing in scientific research comes with a set of assumptions. If the test is applied to data that does not meet those assumptions, then the results of the test may not be valid. The statistics commonly used in genome-wide association studies (GWAS), such as the Fisher’s Exact Test or the Chi-Square Test,… Read more »

A Hitchhiker’s Guide to Next Generation Sequencing – Part 3

         January 19, 2011

The advances in DNA sequencing are another magnificent technological revolution that we’re all excited to be a part of. Similar to how the technology of microprocessors enabled the personalization of computers, or how the new paradigms of web 2.0 redefined how we use the internet, high-throughput sequencing machines are defining and driving a new era of biology. Biologists, geneticists, clinicians,… 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 »

Video Graphics and Genomics: A Real Game Changer?

         October 20, 2010

Why should a genetic researcher care about the latest in video gaming technology? The answer is video graphics cards or Graphics Processing Units (GPUs). For certain computational tasks, a single GPU can perform as well as an entire cluster of CPUs for only a fraction of the cost. And because video gaming has grown into a highly competitive multi-billion dollar… Read more »