Blog

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

3-hour Whole Genome Analysis with GATK4

Vladimir Kovacevic, Teodora Aleksic, Jack DiGiovanna, Stefan Risteski

Science

In the pursuit of accelerating next generation sequencing data processing for clinical applications,  Seven Bridges has developed a configurable GATK4 workflow 3.0 times faster than previous iterations. Following up on our initial push of the GATK4 workflow in 2017, and our recent update with the Broad’s Best Practices, we’ve worked

continue reading

Enabling portable, reproducible, and scalable biomedical data analysis using Rabix Composer and CWL v1.0

Adrian Sharma & Liz Williams

Common Workflow Language, Product News, Reproducibility

We are excited to announce the release of version 1.0 of Rabix Composer, our integrated development environment for creating bioinformatics tools and workflows, and of support for Common Workflow Language (CWL) v1.0 on the Seven Bridges Platform! For an introduction to Rabix Composer and CWL, we encourage you to read

continue reading

Spatial Transcriptomics on the Seven Bridges Platform

Michele Mattioni

Science

As our understanding of biology deepens, many researchers are moving away from bulk gene expression analyses to single-cell analyses. However, current RNA-Seq methods that assay pooled RNA from tissue samples, or even from single cells, fail to conserve the spatial distribution of gene expression within the original tissue. In addition,

continue reading

Smart Variant Filtering

Vladimir Kovacevic

Science

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 major influence on the overall quality. The variant filtering step used to

continue reading

Circulating Tumor DNA Analysis on the Seven Bridges Platform

Sanja Mijalkovic, Luka Topalovic, Ognjen Milicevic

Science

Next Generation Sequencing (NGS) has brought significant improvements in all areas of biotechnology and healthcare — and cancer screening is no exception. The latest game-changer is liquid biopsy, a novel and challenging NGS application. By directly measuring and analyzing circulating tumor DNA (ctDNA) in blood, liquid biopsy is a promising,

continue reading

Try Edico DRAGEN pipelines on Seven Bridges today

Erik Lehnert

Platform

Want to try Edico DRAGEN V2 Pipelines on Seven Bridges? Sign up for our trial before February 19th! Seven Bridges will provide 2-week trial access to our platform for you to try Edico DRAGEN V2 Pipelines. You will receive: Hands-on training with our technical team Up to $20 in credits

continue reading

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

continue reading

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

continue reading

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

continue reading

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