Golden Helix Blog

Turning SRA Files Into Usable BAMs and VCFs

Jan 21, 2014

In our recent webcast, Advancing Agrigenomic Discoveries with Sequencing and GWAS Research, Greta Linse Peterson featured bovine data which she download from the NCBI website. The data was downloaded in SRA format and in order to analyze the data in SVS, the files had to be converted to BAMs and…

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Bringing Powerful Analytic Software to Ontario

Jan 15, 2014

At Golden Helix our number one priority is empowering genetic researchers world-wide with software tools that are as effective as they are robust. So needless to say, we are thrilled to announce a recent collaboration with the Ontario Genomics Institute (OGI), a not-for-profit organization focused on driving and catalyzing the…

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Back to Basics: Importing/Exporting Data in Imputation Program Data Formats with SVS

Dec 31, 2013

In a recent blog post (Comparing BEAGLE, IMPUTE2, and Minimac Imputation Methods for Accuracy, Computation Time, and Memory Usage), Autumn Laughbaum compared three imputation programs. Data can be exported from, or imported into, SVS in the standard file formats for these and other imputation programs. The goal of this blog…

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SVS Workflow Automation Webcast: Your Questions Answered

Sep 20, 2013

Last week, we presented a webcast on Workflow Automation in SVS. If you were unable to attend, a recording of it is on our website. In this post I’ll respond to some of the questions we were unable to answer within the allotted time. Will you provide a link for…

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Guest Post: Finding Rare Pieces of Hay in a Haystack

Aug 19, 2013

Utilizing Identical Twins Discordant for Schizophrenia to Uncover de novo Mutations We are living in exciting times – the reality of high-resolution Cand individual genome sequencing now offers renewed hope in the search for the causes of complex diseases. When this technology is combined with genetic relationships, individual sequences add…

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Comparing BEAGLE, IMPUTE2, and Minimac Imputation Methods for Accuracy, Computation Time, and Memory Usage

Jul 17, 2013

Genotype imputation is a common and useful practice that allows GWAS researchers to analyze untyped SNPs without the cost of genotyping millions of additional SNPs. In the Services Department at Golden Helix, we often perform imputation on client data, and we have our own software preferences for a variety of…

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Vanessa Hayes, PhD and Desiree Petersen, PhD Use Population Genetics to Dig into Mankind’s Roots

Jun 26, 2013

Humans are said to have a 0.1% rate of diversity, seemingly small, but actually quite significant when considering the future of personalized medicine. Gaining a deeper understanding of this genetic variance can help determine susceptibility to disease as well as medicinal response and outcomes. One-third of human genetic diversity can…

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Robert Kleta, MD, PhD and His Newly-Formed Team Publish in The New England Journal of Medicine in a Few Short Months with SVS

May 16, 2013

Thirteen years ago, Dr. Robert Kleta had never heard of a genome-wide association study (GWAS), let alone considered doing one. Now, Dr. Kleta and his colleagues at the University College of London regularly publish articles in The New England Journal of Medicine and other journals on the genetics of rare…

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The Next Phase in Our Evolution

May 8, 2013

Time goes by fast. With the completion of the Human Genome Project in 2003, scientists worldwide were trying to understand the cause and effect of variations in the genome as they relate to functionalities, traits and disease. Along the way, we at Golden Helix helped researchers analyze data, discover variations…

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The Murky Waters of Variant Nomenclature – You Could Be Missing Vital Information

May 6, 2013

When researchers realized they needed a way to report genetic variants in scientific literature using a consistent format, the Human Genome Variation Society (HGVS) mutation nomenclature was developed and quickly became the standard method for describing sequence variations. Increasingly, HGVS nomenclature is being used to describe variants in genetic variant…

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Upcoming Webcast – Knowing Your Downstream: Functional Predictions

May 1, 2013

Presenter: Dr. Bryce Christensen, Statistical Geneticist and Director of Services Date: Wednesday, May 15th, 2013 Time: 12:00 pm EDT Abstract Next-Generation Sequencing analysis workflows typically lead to a list of candidate variants that may or may not be associated with the phenotype of interest. Any given analysis may result in…

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The State of NGS Variant Calling: DON’T PANIC!!

Mar 25, 2013

I’m a believer in the signal. Whole genomes and exomes have lots of signal. Man, is it cool to look at a pile-up and see a mutation as clear as day that you arrived at after filtering through hundreds of thousands or even millions of candidates. When these signals sit…

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Population Structure + Genetic Background + Environment = Mixed Model

Mar 22, 2013

A few months ago, our CEO, Christophe Lambert, directed me toward an interesting commentary published in Nature Reviews Genetics by authors Bjarni J. Vilhjalmsson and Magnus Nordborg.  Population structure is frequently cited as a major source of confounding in GWAS, but the authors of the article suggest that the problems…

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Follow Along on an Analyst’s Journey to Filter Whole Genome Data to Four Candidate Variants in SVS

Mar 14, 2013

Last week Khanh-Nhat Tran-Viet, Manager/Research Analyst II at Duke University, presented the webcast: Insights: Identification of Candidate Variants using Exome Data in Ophthalmic Genetics. (That link has the recording if you are interested in viewing.) In it, Khanh-Nhat highlighted tools available in SVS that might be under used or were…

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Meet Andrew Jesaitis: Software Engineer

Mar 7, 2013

In 2011, I was looking for my next move and happened to attend a lecture given by Gabe Rudy at Montana State University. I was immediately struck by his passion and intelligence about the field of bioinformatics. He ended his talk by mentioning that Golden Helix was hiring, and I…

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Is Illumina Aiming to Compete with its Customers?

Feb 12, 2013

In a recent GenomeWeb article by Tony Fong, “Sequenom’s CEO ‘Puzzled’ by Illumina’s Buy of Verinata, Lays out 2013 Goals at JP Morgan,” Harry Hixson, Sequenom’s CEO, expresses puzzlement over why its major supplier, Illumina, is acquiring a Sequenom competitor in Non-Invasive Prenatal Testing (NIPT), and thus apparently competing with…

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Three New Scripts and Two Updated Ones

Jan 16, 2013

We are excited to let you know about new scripts to aid in filtering rows/columns and identifying unique values in a column, as well as two updated scripts. Don’t forget about the Technical Support Bulletins which keep you up-to-date on all the latest script news. You can stream this feed…

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Meet Autumn Laughbaum: Biostatistician

Jan 9, 2013

As a senior studying statistics at Montana State University, I was fortunate to be granted the opportunity to intern with the development team at a local software company.  I was even more fortunate when this internship turned into full-time employment after I graduated. Working on a team with extremely talented…

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New Plant and Animal Genomes and Tracks Now Available!

Jan 3, 2013

Happy new year! We hope all of our readers, clients, and users had a great holiday season filled with friends and family! While Golden Helix did take a break from blogging in December, we’ve still been pretty busy bringing you new and exciting things. We’re pleased to announce the addition…

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SVS 7.7 is here!

Nov 19, 2012

After much anticipation, we are excited to announce that SVS 7.7 is available! It’s been a lot of work, but we are pleased with the result and know you will be too! SVS 7.7 includes: Improved RNA-Seq Analysis Package for mRNA Expression Profiling Import tabularized quantification data from the Golden…

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