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Workflow Management System

Production-Scale Automation For Complex Genomics Workflows

Comprehensive Capabilities

Edico Genome’s Workflow Management System (WMS) enables users to easily automate their pipelines and workflows on the DRAGEN platform. The WMS integrates sequencing instruments, storage resources, compute resources and workflows with the user’s Laboratory Information Management System (LIMS), creating an end-to-end fully automated process. Users have complete transparency of their samples, lanes, and analysis statuses. The WMS is comprehensive in terms of functional capabilities and users can effortlessly automate their workflows with data from any number of sequencing instruments (of any type) and any number of samples spread across an infinite number of flow cells and lanes.

Push-Button Automation

The production-scale automation process begins with the WMS being configured to monitor the storage locations where the sequencing instruments produce their raw data (BCL files) and detect when output is finished. The WMS then demultiplexes the data and queries the LIMS for information about what analysis to perform on each set of data. Finally, the WMS loads the relevant user-defined workflow onto available DRAGEN systems for analysis and saves the results back on the storage system. After initial set up is complete, the system is designed to be fully “push-button” via an intuitive browser interface – the DRAGEN Web Portal.

Comprehensive Project Management

The WMS utilizes a project-based system for managing data, workflows and available resources. Users can share projects within their organization or across the DRAGEN ecosystem through the management of permission-based access control rules. Each project is maintained with a strict level of security and source data can be utilized by multiple projects without the user incurring duplicate storage footprint.

Single Pane of Glass

Whether using the DRAGEN platform onsite, in the cloud or both, users are able to use a single pane of glass to control all interactions with the WMS. The DRAGEN Web Portal interface is highly responsive, intuitive and accessible via any browser on a server, laptop, tablet or smart phone. Simply drag-and-drop datasets onto workflows and complex processes are initiated.

Monitoring Automated Projects

Automating projects is quick and easy. Users begin by specifying their requirements for the transfer of data from sequencer to the WMS. A sequencer is linked up to a directory that exports all the BCL files, allowing users to monitor specific directories and choose which BCL conversion configuration or app to use. Users can also specify a default analysis app to use for all the samples produced by that sequencer, as well as identify the sequencer output directory for completed analysis files. The WMS also allows users to monitor the progress of each pipeline step of all automated workflows.

WMS API Scripting

The WMS can also be accessed via a fully featured API that enables users to incorporate all of the functionality of the WMS directly into their existing toolchain using simple scripting. The DRAGEN Web Portal makes use of the same WMS API so functionality is identical whether using the API or drag-and-drop interface. A comprehensive API guide is available.

Seamless LIMS Integration

During initial setup, the WMS is connected to the user’s LIMS. The WMS queries the LIMS whenever it detects new data is ready to be processed and extracts a map of samples to lanes and flow cells. Based on that map the WMS will schedule the combining of samples across lanes and flow cells, as well as the analysis of the samples with the relevant workflow indicated by the LIMS.

WMS Demo

Extensive Reporting and Quality Control Metrics

An extensive report as well as Quality Control (QC) metrics for each dataset is available after the completion of the associated workflow. The reporting system includes metrics and graphical representations for mapping/aligning, variant calling, etc. as well as distribution plots, time statistics and many other visualizations that provide meaningful insights and statistics for the user. DRAGEN is able to generate these PICARD, SAMTOOLS, FLAGSTATS and RTG VCFstats type metrics as part of a standard pipeline run.  These reports would traditionally take many hours in addition to the original workflow when executed in software only. In addition, the WMS produces Quality Control metrics that identify potential issues with the sample or sample preparation very early in the analysis process.

Scaling to Production Level

The WMS has been designed to scale from a small lab with a single user with a few gene panels all the way to a population-scale sequencing center with many users generating hundreds of thousands of whole human genomes each year. The system is scalable in terms of file size, number of files, number of sequencing instruments, number of users and number of DRAGEN systems and workflows. It enables production-scale, clinical-grade genomic analysis where users can effortlessly set-up and manage highly complex workflows such as joint genotyping and population calling in minutes. Many of the largest genome sequencing centers in the world use this technology to automate the analysis of tens of thousands of genomes each year.

Advanced Functionality

The WMS includes advanced functionality like the ability to “top-off” existing analysis runs that are found to have insufficient coverage depth. Users can simply top-off the existing analysis with additional reads from a subsequent sequencing run of the same sample and process the combined set of reads as if they originated from the same sequencing run.

Edico Genome is continuously developing new and improved features for the WMS and will continue to make them available to users as part of regular updates. Please contact customer support if you would like to request a specific advanced feature that is not yet supported.

DRAGEN Web Portal

The DRAGEN Web Portal provides a simple, intuitive and easy-to-use interface for the Workflow Management System. Users can also chose to use an API to directly control the WMS via their own scripts.

Customizable Dashboard

The DRAGEN Web Portal includes a fully comprehensive dashboard that enables users to check the statuses of all of there automated tasks at a glance. Each of the dashboard tiles also enables quick access to all of the system features and functionality. The dashboard is customizable and by default includes tiles for displaying lasted info on projects, analyses, data used, storage used and available applications/workflows.

Single Drag and Drop Interface

In addition to full automation, the DRAGEN Web Portal also enables users to simply drag-and-drop data files from their projects onto desired workflows to initiate the otherwise complex process of managing resources and executing an analysis. Drag-and-drop pipeline development and scheduling are available through the DRAGEN Web Portal with the purchase of any DRAGEN license. The WMS capabilities as described in this brief are available with the purchase of the WMS, which is then made accessible through the web portal.

Product Sheet