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

DRAGEN on Seven Bridges: Ultra-Rapid NGS in the Cloud

Seven Bridges recently announced its partnership with Edico to provide Edico’s DRAGENTM genomic analysis pipelines on our secure, collaborative biomedical data platform. Please join us on January 24th, 1-2 PM ET for a webinar covering the DRAGENTM Germline V2, Somatic V2, and RNA Gene Fusion Detection pipelines now available on …

Written by Erik Lehnert

The GA4GH Workflow Execution Challenge: evaluating reproducibility and portability across platforms

Large-scale, geographically distributed genomics analysis efforts, such as the PanCancer Analysis of Whole Genomes (PCAWG) project, highlight a trend in our community towards moving compute to where data resides. For PCAWG, this was out of necessity as the genomes for ~2,800 cancer donors were stored across 8 different locations around …

Written by Guest Author: Brian O’Connor

The Cancer Genomics Cloud: collaborative, reproducible, democratized (and now citable!)

Last week we published our paper The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized—A New Paradigm in Large-Scale Computational Research in Cancer Research as part of their special issue on computer resources. Congratulations to everyone who’s worked on the Cancer Genomics Cloud, and many many thanks to the team at …

Written by Nick

Develop, test and scale reproducible bioinformatics workflows with Rabix

Rabix: the toolkit for reproducible bioinformatics This summer, our development team announced the public launch of Rabix: the open source toolkit for creating and running reproducible computational workflows. Rabix was founded to overcome the challenges inherent in running reproducible bioinformatics analyses at scale. Here we show how the combination of software containers, workflow language and Rabix gives bioinformaticians the […]

Written by Nick

Big data for big results in childhood cancer

Last week Seven Bridges CEO Brandi Davis-Dusenbery joined an expert panel to discuss how data contributes to the fight against childhood cancer. Hosted by The Atlantic, the Children and Cancer forum sought to address the practical realities of pediatric cancer and identify ways to improve outcomes for these patients. You …

Written by Nick

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

Reducing bioinformatic analysis costs with AWS Spot instances

Although genome sequencing costs have dropped dramatically over the past few years, analyzing large amounts of genomic data remains expensive. As the scale of genomic projects continues to grow, cost-efficient bioinformatic analysis is key to gaining insight from the estimated 100 million to 2 billion human genomes that will be …

Written by Jessica Lau

CloudNeo: CWL Brings Cancer Genomics to the Cloud

A cloud-based workflow for patient-specific tumor neoantigens CloudNeo—a computational workflow for identifying patient-specific tumor neoantigens from Next-Generation Sequencing (NGS) data, was recently published in Bioinformatics. Originating from Jeffrey Chuang’s lab at The Jackson Laboratory, CloudNeo is a neoantigen prioritization workflow designed specifically for the cloud. The authors have made the CloudNeo workflow available on the Seven […]

Written by Patrick

Sequence Bloom Trees, Part I: Motivation and principles

Modern bioinformatics involves a lot of searching datasets, like The Cancer Genome Atlas (TCGA), that contain data from many experiments. Wanting to do this efficiently raises not only data management problems but also algorithmic ones. Searching a dataset like TCGA in hopes of figuring out which experiments contain a given …

Written by Nate

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.

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