Stanford Sequencing Center analysis workflow on DNAnexus

A cloud-based sequencing pipeline: bringing people and analyses to data

The Stanford Center for Genomics and Personalized Medicine (SCGPM) high-throughput cloud sequencing pipeline delivers mapped sequencing reads and detailed quality-control metrics, on the DNAnexus cloud genome informatics platform. Sequencing data are delivered directly to a unified cloud informatics platform that provides storage, compute, and access to popular bioinformatics tools. From that platform, data can be shared with collaborators around the world or plugged directly into downstream analyses. Many shared resources for processing sequencing data, such as ENCODE Consortium workflows for analyzing Methyl-seq, ChIP-seq, and RNA-seq data are publicly available on DNAnexus, as well as tools for generating custom workflows. All of these tools for managing, sharing, and analyzing data are accessible through an easy-to-use web interface or command-line console. By delivering sequencing data on an intuitive cloud informatics platform, we are breaking down barriers between data generators and analysts, and making bioinformatics accessible to novices and experts alike. 

SCGPM provides sequencing for several dozen labs at Stanford in addition to researchers at USC, Yale, the University of Chicago and a growing list of research facilities supported by CIRM Center for Excellence in Stem Cell Research (UCSF, UCLA, UCSD, UCSC, Scripps Research Institute, J. Craig Venter Institute, Ludwig Cancer Research, Salk Institute). SCGPM is capable of sequencing over 3000 genomes or 22,000 exomes every year.

2016 Workshop

Stanford Center for Genomics and Personalized Medicine (SCGPM) and DNAnexus hosted an interactive workshop demonstrating how to use the DNAnexus cloud genomics platform to easily perform an array of common bioinformatics tasks. 

 

Schedule

  • 09:00 - 09:30 AM : Registration
  • 09:30 - 10:00 AM: Introduction and background
  • 10:00 - 11:00 AM: Using the DNAnexus Web UI
  • 11:00 - 11:15 AM: Coffee break
  • 11:15 - 12:00 PM: RNA-seq analysis on DNAnexus - Ramesh Nair, SCGPM
  • 12:00 - 01:30 PM: Lunch
  • 01:30 - 02:00 PM: Liquid Biopsy: The Next Gold Standard for Diagnosis - Raheleh Salari, Natera
  • 02:00 - 03:00 PM: Using DNAnexus Command Line Interface
  • 03:00 - 03:15 PM: Coffee & Cookies
  • 03:15 - 03:45 PM: Moving Diagnostics into the Cloud: A Clinical-Grade NGS Test to Monitor cfDNA for Solid Organ Transplant... and Beyond - David Ross, CareDx
  • 03:45 - 04:45 PM: Building an applet on DNAnexus
  • 04:45 - 05:00 PM: Closing statement
  • 05:00 - 06:00 PM: Happy hour

 

Workshop Leaders from DNAnexus

Maria Simbirksy, Scientist at DNAnexus, will present how to interact with the Platform through the web UI. Maria works on Scientific Partnerships at DNAnexus. 

Naina Thangaraj, Bioinformatician at DNAnexus, will demonstrate how to use the command line. Naina works with customers to train them on DNAnexus and implement pipelines on the Platform. 

Singer Ma, Scientist at DNAnexus, will walk you through building a custom applet on the Platform. Singer has worked with large-scale analysis projects such as The Cancer Genome Atlas, the International Cancer Genome Consortium, and the Cohorts for Heart and Aging Research in Epidemiology.

 

Speakers

Ramesh Nair, PhD, is the Associate Director of Bioinformatics at Stanford Center for Genomics and Personalized Medicine. He will be discussing RNA-sequencing analysis on DNAnexus.  

Raheleh Salari, PhD, Bioinformatics Manager at Natera, will be presenting "Liquid Biopsy: The Next Gold Standard for Diagnosis". Natera is a genetic testing and diagnostics company in San Carlos that develops non-invasive methods for analyzing DNA. 

David Ross, PhD, Senior Director of Bioinformatics at CareDx, will discuss "Moving Diagnostics into the Cloud: A Clinical-Grade NGS Test to Monitor Cell-Free DNA for Solid Organ Transplant". CareDx is a molecular diagnostics company dedicated to improving the lives of organ transplant patients through noninvasive diagnostics. The company is located in Brisbane, California. 

 

Videos

Using DNAnexus Web User Interface

Maria Simbirksy, Scientist at DNAnexus, presents how to interact with the Platform through the web UI. 

Using DNAnexus Command Line Interface

Naina Thangaraj, Bioinformatician at DNAnexus, demonstrates how to use the command line.

Building an applet on DNAnexus

Singer Ma, Scientist at DNAnexus, walks us through building a custom applet on the Platform.

RNA-Seq Deep Dive

Ramesh Nair, PhD, Associate Director of Bioinformatics at Stanford Center for Genomics and Personalized Medicine, does a deep dive on RNA-sequencing analysis.

Workshop Organizer

Paul Billing-Ross, MS

Paul is SCGPM software developer responsible for the migration of our sequencing informatics workflow from our on-premise HPC cluster to DNAnexus Cloud. 

He is passionate about building the roads and bridges of genomics research. He broke into computational biology studying models of molecular evolution under Dr. Sudhir Kumar at Arizona State University and then transitioned to studying mitochondrial genetics as an NSF Graduate Research Fellow at Cornell University.