Blog

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

Erik Lehnert

Platform, Seminars

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

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

Guest Author: Brian O’Connor

Science

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

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Develop, test and scale reproducible bioinformatics workflows with Rabix

Nick

Common Workflow Language, Reproducibility

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

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Big data for big results in childhood cancer

Nick

Cavatica, Useful Data

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

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A first look at GATK4 on the Seven Bridges Platform

Nick

Genomics, 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

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CloudNeo: CWL Brings Cancer Genomics to the Cloud

Patrick

Cancer Genomics Cloud, Common Workflow Language

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

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Sequence Bloom Trees, Part I: Motivation and principles

Nate

Science

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

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Custom interactive analysis on all Seven Bridges environments

Jessica Lau

Cancer Genomics Cloud, Cavatica, Platform, Product News

This week we released Data Cruncher, an interactive analysis tool available on the Seven Bridges Platform, Cancer Genomics Cloud, and Cavatica. By enabling researchers to apply custom scripts in JupyterLab to data stored in the cloud, Data Cruncher supports interactive and collaborative bioinformatic analysis at scale. Bringing custom interactive analysis to the cloud Although some

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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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