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Promoting Interoperability and Standardization: Seven Bridges and GA4GH

The Global Alliance for Genomics and Health (GA4GH) is an international body set to create policies and promote technical standards to maximize interoperability among various stakeholders involved with genomics and healthcare-related data. Through its engagement in GA4GH, Seven Bridges actively works with platform development partners and industry leaders to develop …

Written by Dan Ventre

The Annotation Explorer: 1 billion variants, hundreds of annotations, and just a few minutes

With the ongoing proliferation of genome sequencing data, the number of rare variants found is growing rapidly. To detect associations between phenotypes of interest and these rare variants, researchers employ mechanisms to increase statistical power in association testing. Variant annotation information can be used to combine variants into biologically-relevant units …

Written by Dan Ventre

Single and Multiple Variant Association Testing on Seven Bridges

For researchers interested in performing genotype-phenotype association studies, Seven Bridges offers a suite of tools for both single-variant and multiple-variant association testing. These tools and features include EPACTS, PLINK, and the GENESIS pipelines. EPACTS EPACTS (Efficient and Parallelizable Association Container Toolbox) is a versatile software pipeline to perform various statistical …

Written by Dan Ventre, Alison Leaf, Dave Roberson, Ana Stankovic, and Aleksandar Danicic

GATK Best Practice: RNA-seq Variant Calling Workflow on the Seven Bridges Platform

Whether or not variant calling should be performed on RNA-seq data and its possible benefits is a debatable topic. One thing is for certain, if you have already sequenced the transcriptome with the intent to analyze gene expression, but you are also interested in exploring variants existing in the same …

Written by Nemanja Vucic

Assessing State of the Art Bioinformatics

The Oxford English Dictionary defines bioinformatics as “the science of information and information flow in biological systems, especially of the use of computational methods in genetics and genomics.” In common vernacular, it is often defined as the use of statistical and computing methods to solve or better understand complex biological …

Written by Vladimir Kovacevic

BioCompute and Its Importance in Accelerating Market Access for New Drugs

The prevalence of NGS data within regulatory submissions has skyrocketed over the past few years which has prompted a collaboration amongst the Food and Drug Administration (FDA) and George Washington University to develop the BioCompute Object (BCO) as a standard for communicating NGS data. The BioCompute Object community aims to …

Written by Dennis Dean

Taxanomic Profiling of Metagenomics Samples

Numerous colonies of different organisms live virtually everywhere on Earth, even in and on our bodies. They are called microbes and we think we know all about them. But do we really? Actually, the human race knew nothing about microbes before the 17th century. There were some assumptions and hypotheses, …

Written by Aleksandar Danicic, Nemanja Vucic, Srdjan Kasapovic and Vesna Pajic

A first look at GATK4 on the Seven Bridges Platform

One of the big take-away messages from the Bio-It World Conference this year was the Broad Institute’s announcement that they plan to fully open source their GATK4 software. By transitioning to a BSD 3-Clause licence, GATK4 becomes fully open for commercial use without a separate commercial licence, which should particularly …

Written by Nick

Identifying viral sequences in TCGA data using Kraken and Centrifuge

Image adapted from Kim et al. Genome Res. 26, 1721–1729 (2016). Next-Generation Sequencing has opened up the field of metagenomics. In metagenomic studies, a sample often contains a complex ecosystem of different microorganisms. The key challenge in these experiments is disentangling the identities of unknown species from millions of sequencing reads. Bioinformatic tools for metagenomics are designed to […]

Written by Patrick

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