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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

Work Smarter, Not Harder: CWL and the Seven Bridges platforms

Seven Bridges is committed to ensuring reproducibility and portability of research analysis, and the use of Common Workflow Language (CWL) for tool and workflow descriptions helps to facilitate both. CWL is an open-source, community-driven specification and emerging standard for describing how to run computational analysis with command line tools in …

Written by Dan Ventre

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

Enabling Workflow Reproducibility in the Cloud with New Pipelines from the Genomic Data Commons

When analyzing genomic data, there is a vast range of bioinformatics tools and workflows to choose from. However, making an informed selection from so many options can be overwhelming, even within a relatively narrow topic, such as harmonization to a reference genome. One approach to selecting the right tool for …

Written by Manisha Ray

Bioinformatics Workflow Portability is Critical to Achieving Reproducibility

With the explosion of genomic data in recent years, the number of bioinformatics workflows has seen a corresponding proliferation. Researchers and developers now have a wealth of analysis options, from building their own tools to taking advantage of those developed by others. However, a workflow developed in one environment may …

Written by Manisha Ray

How to Use Variant Filtering for Genomic Analysis

The variant filtering process consists of selecting highly confident variants and removing the ones that are falsely called. Secondary genomic DNA analysis is mainly oriented toward alignment and variant calling, assuming the accuracy of these two would provide a major influence on the overall quality. The variant filtering step used …

Written by Vladimir Kovacevic

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