blog

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

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

continue reading

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

continue reading

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

continue reading

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

continue reading

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

continue reading

Optimizing novoBreak on the Cancer Genomics Cloud

Jessica Lau

Cancer Genomics Cloud

Last week, we released novoBreak—an exciting new bioinformatics software—on the Cancer Genomics Cloud (CGC). The tool, described by Zechen Chong and colleagues in Nature Methods, is a novel approach to detect breakpoints in cancer genomes with high precision and sensitivity. In this post, we explain how Zechen used the Publish your app

continue reading

Cavatica wins Bio-IT People’s Choice Award

Patrick

Cavatica, Product News, Useful Data

Cavatica is the data sharing platform for pediatric disease Seven Bridges and our partners at The Children’s Brain Tumor Tissue Consortium (CBTTC) and the Pacific Pediatric Neuro-Oncology Consortium (PNOC) were honored with a Bio-IT World People’s Choice award for Cavatica, the collaborative analysis and data sharing platform for pediatric diseases. This award follows Seven Bridges’ previous Best

continue reading

Identifying viral sequences in TCGA data using Kraken and Centrifuge

Patrick

Genomics, Science

Image adapted from Kim et al. Genome Res. 26, 1721–1729 (2016). Next-Generation Sequencing has opened up the field of metagenomics. In metagenomic studies, a sample often contains a complex ecosystem of different microorganisms. The key challenge in these experiments is disentangling the identities of unknown species from millions of sequencing reads. Bioinformatic tools for metagenomics are designed to

continue reading

Reference bias: Challenges and solutions

Jessica Lau

Conferences, Graph Genome, Science

Ahead of the Bio-IT World Conference & Expo in Boston this week, we take a look at the role of reference genomes in ensuring accurate genomic analysis. In standard next-generation sequencing analyses, DNA is fragmented and sequenced. The sequenced reads are then aligned to a reference genome for the species.

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