Tag Archives: GenomeBrowse

Advanced Techniques for GenomeBrowse Customization

         January 23, 2024

Today, we will be exploring the indispensable role of GenomeBrowse in your VarSeq workflows. This blog aims to guide you through various customization options, including color preferences, filtering techniques, display modifications, numeric value plotting, and additional tips. I hope to enhance your GenomeBrowse experience and enable you to gain valuable insights into your data. Let’s jump in by talking about… Read more »

Auto Computation of Coverage Files

         January 18, 2024

The latest VarSeq release offers enhanced control over genome browse visualization computations. These computations, which are responsible for computing and caching the aggregate view of tracks within GenomeBrowse, are now more flexible. Typically, these tracks create files with the “.covtsf” extension and are used for zoomed-out density views of sources like VCFs and BAMs. Previously, the computation would commence automatically… Read more »

Getting the most out of variant visualizations in GenomeBrowse

         June 29, 2022

Genomic data visualization is an extremely powerful means to help users comprehend massive amounts of sequencing data and is valuable for communicating genomic information and findings. Genome browser tools allow users to visualize aligned sequence data in BAM format, map the data to a reference assembly, view annotation tracks, genomic region tracks, export graphics for sharing, and much more. Genome… Read more »

Mining VarSeq Curated Databases for Literature – Raw Data Search in Variant Table or GenomeBrowse

         April 21, 2022

An under-utilized use of VarSeq is the ability of mining raw variant data in GenomeBrowse for relevant literature. By bringing in various public and private annotation sources, GenomeBrowse allows the user to interface with raw variant data in a compressed and manageable view. This blog will show you how to leverage these sources to power up your search for variant… Read more »

Customer Publications February 2022

         February 28, 2022
customer pubs feb 2022

VarSeq software again takes center stage in our recent publications for February. It is our great honor to be a part of the groundbreaking discoveries highlighted below as well as the many others too numerous to include in this blog post! We are happy to contribute to scientific findings from all our analysis platforms, but we are especially proud of… Read more »

Advanced Plotting Capabilities with GenomeBrowse

         September 22, 2020

In this blog update, I’ll be walking you through some of the advanced plotting capabilities with GenomeBrowse. The strategy with any next-gen sequencing analysis is to filter down to interesting variants for either research or clinical conclusion. Golden Helix produces powerful software specifically tailored for this efficient and comprehensive search for interesting and clinically relevant variants. One additional advantage of… Read more »

Analyze Your 23andMe Genotype Files with Golden Helix

         July 22, 2015
23andMe

I was definitely an early adopter when it comes to personal genomics. In a recent email to their customer base announcing their one millionth customer, they revealed that I was customer #44,299. And I have been consistently impressed with the product 23andMe provides through their web interface to make your hundreds of thousands of genotyped SNPs accessible and useful. It… Read more »

The Clinical Genome Conference 2015 Highlights

         June 30, 2015

This last week I had the pleasure of attending the fourth annual Clinical Genome Conference (TCGC) in Japantown, San Francisco and kicking off the conference by teaching a short course on Personal Genomics Variant Analysis and Interpretation. Some highlights of the conference from my perspective: Talking about clinical genomics is no longer a wonder-fest of individual case studies, but a… Read more »

New and Updated Annotation Tracks Now Available!

         June 11, 2015

In recent months we have been updating our public annotation library to include the most recent versions of existing sources as well as include new sources. Each of these annotation sources are compatible with our three major products (SVS, GenomeBrowse and VarSeq) and can be used for visualization, annotation and filtering. NHLBI ESP6500SI-V2-SSA137 Exomes Variant Frequencies 0.0.30, GHI Annotations are… Read more »

Visually Filtering Data in GenomeBrowse

         April 16, 2015

Over 650 GenomeBrowse licenses have been registered and downloaded since the beginning of 2015, and with so many people enjoying the utility of this freeware program, I wanted to showcase some advanced tips and tricks so you can get more out of GenomeBrowse! Under the Controls panel, when you’re clicked inside a data plot, there is a “Filter” tab. This… Read more »

New Plugin for Ion Torrent Server

         October 21, 2014

Golden Helix is proud to announce the release of the Golden Helix GenomeBrowse Plugin for Ion Torrent server. The new plug-in enables adding selected BAM files from Torrent Server reports directly into GenomeBrowse. The BAM files remain on the torrent server and are streamed from the server on demand using your credentials. This feature allows GenomeBrowse users to visualize genomic… Read more »

Updates to ClinVar and dbSNPs: Fresh charts for Cromonaughts!

         August 28, 2014

I’m sitting in the Smithsonian Air and Space Museum basking in the incredible product of human innovation and the hard work of countless engineers. My volunteer tour guide started us off at the Wright brother’s fliers and made a point of saying it was only 65 years from lift off at Kitty Hawk to the landing of a man on the moon…. Read more »

Have you ever had a bad experience with a VCF file?

         August 5, 2014

“Who has ever had a bad experience with a VCF file?” I like to ask that question to the audience when I present data analysis workshops for Golden Helix. The question invariably draws laughter as many people raise their hands in the affirmative. It seems that just about everybody who has ever worked VCF files has encountered some sort of… Read more »

The added value of GenomeBrowse

         July 17, 2014

We released GenomeBrowse 2.0 earlier this year, allowing users to review all types of genomic data. Since then, it has received rave reviews from thousands of users around the world. Essentially, it’s the Google Earth app for genomic data. GenomeBrowse allows a user to sift through vast amounts of genomic data, and make it easy to focus on a single part… Read more »