Blog

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

Single and Multiple Variant Association Testing on Seven Bridges

For researchers interested in performing genotype-phenotype association studies, Seven Bridges offers a suite of tools for both single-variant and multiple-variant association testing. These tools and features include EPACTS, PLINK, and the GENESIS pipelines. EPACTS EPACTS (Efficient and Parallelizable Association Container Toolbox) is a versatile software pipeline to perform various statistical …

Written by Dan Ventre, Alison Leaf, Dave Roberson, Ana Stankovic, and Aleksandar Danicic

Multi-Omic Analysis at the Push of a Button

Increasing the simplicity and efficiency of running data analysis workflows in a consistent manner across a diverse set of users is a challenge faced by many biotech, diagnostic, and pharmaceutical companies. Manually gathering compatible input files from disparate sources, curating file metadata, starting multiple consecutive compute tasks, dealing with transient …

Written by Christian Frech

Harnessing the Cloud for Single-cell Research with the Seven Bridges Platforms

What is single-cell RNA sequencing analysis (scRNA-Seq)? The popularity of single-cell methodologies has seen an exponential rise in recent years.  Around 2010, the state of the art was examining only one cell by single-cell transcriptomics methods. Now we have the technology to analyze hundreds of thousands of cells in a …

Written by Daniel Ventre, Manisha Ray, Nemanja Vucic

Work Smarter, Not Harder: CWL and the Seven Bridges platforms

Seven Bridges is committed to ensuring reproducibility and portability of research analysis, and the use of Common Workflow Language (CWL) for tool and workflow descriptions helps to facilitate both. CWL is an open-source, community-driven specification and emerging standard for describing how to run computational analysis with command line tools in …

Written by Dan Ventre

Pan-Genome Graphs Help Identify SNPs, INDELs and Structural Variants with Higher Accuracy

Improved methods for analyzing next-generation sequencing (NGS) data is mission critical given inherent flaws with the current human genome linear reference. Building on years of experience developing pan-genome references to eliminate reference bias, Seven Bridges GRAF is now broadly available to researchers on all Seven Bridges platforms.  The next-generation Seven …

Written by H. Serhat Tetikol, Amit Jain, Seven Bridges GRAF Team

What Makes TOPMed Datasets So Special?

Studies from the Trans-Omics for Precision Medicine (​TOPMed​) program are available for analysis on NHLBI BioData Catalyst. The TOPMed program, funded by the National Heart, Lung, and Blood Institute (NHLBI), part of the National Institutes of Health (NIH), focuses on data specifically for advancing science in the fields of heart, …

Written by Daniel Ventre

Seven Bridges Selected to Build Cancer Data Aggregator for the National Cancer Institute as Part of Consortium Led by the Broad Institute

Cancer research is one of the most dynamic applications of precision medicine. However, the collection of tumor and patient genomic sequences, protein biomarkers, tumor cells, radiological and molecular images and clinical findings creates a superabundance of data held in various datasets in different repositories across the country and around the …

Written by Jack DiGiovanna

GATK Best Practice: RNA-seq Variant Calling Workflow on the Seven Bridges Platform

Whether or not variant calling should be performed on RNA-seq data and its possible benefits is a debatable topic. One thing is for certain, if you have already sequenced the transcriptome with the intent to analyze gene expression, but you are also interested in exploring variants existing in the same …

Written by Nemanja Vucic

Assessing State of the Art Bioinformatics

The Oxford English Dictionary defines bioinformatics as “the science of information and information flow in biological systems, especially of the use of computational methods in genetics and genomics.” In common vernacular, it is often defined as the use of statistical and computing methods to solve or better understand complex biological …

Written by Vladimir Kovacevic

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