Blog

We blog about genomics. We also make a platform for open-source analysis of next generation data in the cloud. Hello.

Pan-Genome Graphs Help Identify SNPs, INDELs and Structural Variants with Higher Accuracy

Improved methods for analyzing next-generation sequencing (NGS) data is mission critical given inherent flaws with the current human genome linear reference. Building on years of experience developing pan-genome references to eliminate reference bias, Seven Bridges GRAF is now broadly available to researchers on all Seven Bridges platforms.  The next-generation Seven …

Written by H. Serhat Tetikol, Amit Jain, Seven Bridges GRAF Team

What Makes TOPMed Datasets So Special?

Studies from the Trans-Omics for Precision Medicine (​TOPMed​) program are available for analysis on NHLBI BioData Catalyst. The TOPMed program, funded by the National Heart, Lung, and Blood Institute (NHLBI), part of the National Institutes of Health (NIH), focuses on data specifically for advancing science in the fields of heart, …

Written by Daniel Ventre

Seven Bridges Selected to Build Cancer Data Aggregator for the National Cancer Institute as Part of Consortium Led by the Broad Institute

Cancer research is one of the most dynamic applications of precision medicine. However, the collection of tumor and patient genomic sequences, protein biomarkers, tumor cells, radiological and molecular images and clinical findings creates a superabundance of data held in various datasets in different repositories across the country and around the …

Written by Jack DiGiovanna

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

Be Cloud-Agnostic: A Solution for Computing on Genomics Datasets in Distributed Cloud Locations

The Multi-Cloud features on the Seven Bridges Platform allow you to work in a “cloud-agnostic” manner, enabling researchers to access and compute on datasets stored on multiple cloud locations to save time and money.  Empower your research with relevant datasets regardless of where the data lives  Starting a research project with data distributed in multi-cloud […]

Written by Daniel Ventre

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 Memoization Enhances Efficiency for Large Scale Genomic Analysis Research Projects

Memoization for large scale genomic analysis allows researchers and bioinformaticians to restart from a point of failure by enabling the reuse of existing outputs. This functionality is of critical importance given the size and complexity of genomic data and the impact of a failure on workflow efficiency and overall cost. …

Written by The Seven Bridges Computation Team

We are always engaged in research and development, working to build the future of genomics, science, and health. Let's work together. We'd love to hear about your projects and challenges, so drop us a line. get in touch