Blog

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

Custom interactive analysis on all Seven Bridges environments

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 […]

Written by Jessica Lau

Optimizing novoBreak on the 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 …

Written by Jessica Lau

Cavatica wins Bio-IT People’s Choice Award

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 […]

Written by Patrick

Identifying viral sequences in TCGA data using Kraken and Centrifuge

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 […]

Written by Patrick

Reference bias: Challenges and solutions

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. …

Written by Jessica Lau

Simons Genome Diversity Project now available on the Platform and CGC

We’ve just announced the availability of the Simons Genome Diversity Project (SGDP) dataset on our Platform and Cancer Genomics Cloud. In keeping with Seven Bridges’ mission to colocalize data and analysis tools on the cloud, anyone with an internet connection can now explore SGDP’s 35TB of data. One way to …

Written by Patrick

Data democratization advances oncology research

Next week Seven Bridges will be at the Molecular Medicine Tri-Conference in San Francisco, California. Gaurav Kaushik, one of our Scientific Program Managers, will be sharing our work on the Cancer Genomics Cloud (CGC) as part of the conference’s informatics track. Launched publicly in 2016, the Seven Bridges CGC is …

Written by Jessica Lau

Creating a bulletproof workflow

We’ve interviewed some of Seven Bridges’ experienced bioinformaticians to collect their tips and best practices for creating a bulletproof workflow on the Platform. Many bioinformaticians will have experienced the frustration of inexplicably failed analyses, incorrect outputs, or inconsistent results. When dealing with complex tools and gigabytes or even terabytes of …

Written by Marko Marinkovic

Festival of Genomics: Reflecting on graph genomes

Yesterday at Festival of Genomics, London, Seven Bridges CEO Deniz Kural joined a panel discussing implementations of graph genomes, alongside Erik Garrison from the Wellcome Trust Sanger Institute and Andy Yates from EMBL-EBI. Great panel talking about #graph #genomes at #GenomicsFest @erikgarrison @denizkural Andrew Yates @FLGenomics pic.twitter.com/4Cxy2CslvT — Adrian Alexa …

Written by Nick

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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