Here at Golden Helix, we’ve sought to develop top-quality bioinformatic software to handle not only high-throughput clinical next-gen sequencing pipelines but also cater to research groups exploring their cohorts. Our tools fit in this NGS pipeline by importing the VCF and BAM files for downstream filtration, annotation, and classification/interpretation as well as clinical reporting. It was obvious early on and… Read more »
The first two blogs in this series covered Sentieon’s somatic variant calling from Tumor with Normal (Part I) and Tumor without Normal (Part II). In addition to providing multiple somatic variant calling processes, users also have access to high-sensitivity scripts and full support for the GRCh38 reference assembly. Without going into excessive detail, this final blog of the series will… Read more »
To recap what we have covered in this blog series thus far, Sentieon allows users to call somatic variants against a matched normal sample and a tumor-only analysis. Part I of this series covered the variant calling workflow for tumors with matching normal samples. However, a common situation would be to call variants for a tumor sample without the normal…. Read more »
As I mentioned in the first part of this series, Sentieon allows users to call somatic variants against a matched normal sample and a tumor-only analysis. Utilization of a Tumor-Normal Workflow In addition to the fundamental process of alignment and variant calling, there are a few more steps that will improve the quality of your secondary analysis. Figure 1 (below)… Read more »
Sentieon has become well known for the dramatic improvements it supplies in speed and accuracy for secondary analysis. Luckily, these improvements are not only available for DNAseq germline based variants but also for TNSeq somatic investigation. Sentieon has proven the capability by leading in awards such as the ICGC-TCGA DREAM Challenge for SNVs, Indel, and structural variants. This value not… Read more »
Customers are always asking for ways to improve their experience with Sentieon, our partner’s secondary analysis tools that process genomics data with high computing efficiency, fast turnaround time, exceptional accuracy and 100% consistency. We have a few tips to get the most out of Sentieon. In this article I will be going over: Basic system requirements Custom scripts vs default… Read more »
Secondary Analysis with Sentieon: Rapid and Accurate Variant Calling This blog post will cover the utilization of secondary analysis tools to produce a list of high-quality variants and associated coverage data. This data will serve as the main, importable content for the tertiary stage of analysis where variants are interpreted and classified for their impact on a patients’ disorder. We… Read more »
Sentieon develops bioinformatics secondary analysis tools to process genomic data with high computing efficiency, fast turnaround time, exceptional accuracy and 100% consistency. These features are what led to the partnership of Golden Helix and Sentieon to provide users with a comprehensive solution for genomic data analysis. This blog post gives readers a more detailed understanding of the top five features… Read more »
Creating Custom Scripts The first part of the Getting Started Guide for Sentieon described the steps for downloading the Sentieon tools, acquiring a license file, and running the example script/pipeline to generate the VCF and BAM files. This blog will cover some custom script changes users can make to add more efficiency when running through multiple samples at once. We… Read more »
Sentieon; your swift secondary analysis solution. Golden Helix’s software solutions present a reputable and top-quality analysis of your NGS data. Looking at this process from a 30,000 ft view, the annotation and filtering of variants in your vcf files and discovery of CNVs based coverage data in the bam file make up the tertiary level portion of the analysis. However,… Read more »
Sentieon TNscope is a platform dedicated to the identification of tumor-normal somatic variants including single nucleotide variation (SNV), indel, as well as structure variations (SVs). In our recent webcast, Dr. Donald Freed, Bioinformatics Scientist at Sentieon, gave viewers an exclusive overview of the platform. The webcast generated a lot of great questions which I would like to share with you… Read more »
We find ourselves talking about our partnership with Sentieon, a lot! More specifically, we are always extolling the powerful, comprehensive genomic data analysis solution we are able to offer our clients. Sentieon’s Secondary Analysis Suite made a significant improvement in runtime over BWA-MEM, GATK, Mutect, and MuTect2 while providing deterministic and identical results. Here are two fantastic white papers that… Read more »
Today, we are happy to announce a multi-year partnership with Sentieon, a company that develops bioinformatics secondary analysis tools to process genomic data. This partnership will integrate Sentieon’s secondary analysis tools with Golden Helix software to provide users with a comprehensive solution for genomic data analysis. Sentieon’s suite of secondary analysis tools made the significant improvement in runtime over BWA-MEM, GATK,… Read more »
