case-study

Case Study: NatureMetrics Standardizes Complex NGS Workflows That Turn Nature Into Data with Sapio LIMS

Executive Summary

NatureMetrics , a world leader in nature data and intelligence, adopted the modern, unified LIMS platform from Sapio Sciences to manage its unique and complex next-generation sequencing (NGS) workflows. By leveraging cutting-edge eDNA technology, NatureMetrics generates large-scale biodiversity data for global sustainability and conservation.

The Sapio LIMS has enabled NatureMetrics to adopt an end-to-end material, instrument, and sample management workflow out-of-the-box; track samples through complex processes; and streamline decision-making and sample routing by automating key elements of quality control, moving beyond fragmented spreadsheets.

The Customer: NatureMetrics

Company Overview

NatureMetrics is a global nature intelligence technology company providing an end-to-end nature-monitoring and impact-reporting solution. The company’s Nature Intelligence Platform, powered by eDNA, transforms species data at the site level into meaningful insights to manage and monitor nature and biodiversity. NatureMetrics’ services, which include a robust platform for impact monitoring and reporting along with strategy development and survey capabilities, enable businesses to manage their impacts and dependencies on biodiversity at scale, converting the complexities of nature into simple insights to inform decisions about how operations affect the environment, conservation, and sustainability. The company’s technology has supported biomonitoring around the world, including mining projects in West Africa, conservation projects in the Amazon rainforest, and renewable energy infrastructure projects in the UK.

Background

Over time, NatureMetrics had accumulated a collection of interconnected spreadsheets and databases to manage its various sequencing workflows. “We developed somewhat clever methods of interlinking between spreadsheets and built dashboards to help manage processes,” said Dr. Andrew Briscoe, Science Director at NatureMetrics.

The Challenge: Scaling Complex NGS Workflows Beyond Spreadsheets

As NatureMetrics scaled, its existing spreadsheet and database system quickly became a limiting factor when as many as 40 NatureMetrics scientists needed to access data simultaneously. Plus, said Dr. Briscoe, the spreadsheets did not have the appropriate data integrity NatureMetrics required. Moreover, the inherent complexity of the existing databases spawned additional fit-for-purpose but siloed satellite spreadsheets that were difficult to (automatically) draw insights from.

The Solution: Sapio LIMS for NGS Workflow Standardization

Why Sapio Sciences Was Chosen

NatureMetrics initially looked at 15 different laboratory information management systems (LIMS) as it sought a modern informatics solution. Five contenders were evaluated by the NatureMetrics LIMS working group, and three finalists were put through their paces to see which would be best suited to NatureMetrics’ unique needs.

NatureMetrics selected Sapio’s platform, which unifies a LIMS, electronic laboratory notebook (ELN), and scientific data management solution in the cloud. “The openness and flexibility of the Sapio solution impressed us, and the low-code/no-code system has enabled us to define standard processes and, importantly, make changes as our needs and technology evolve,” said Dr. Briscoe.

Implementation Overview

Currently, the Sapio system supports around 50 scientists working in two labs located in the United Kingdom and Canada. To take the system live, NatureMetrics ran the Sapio platform alongside the company’s old systems, which not only helped with training but also enabled NatureMetrics to catch any remaining bugs and issues during rollout.

Key Features

• Unified LIMS Platform: A modern, unified platform incorporating LIMS, ELN, and a scientific data management solution in the cloud.
• Low-Code/No-Code System: Enables defining standard processes and making changes as needs and technology evolve.
• End-to-End Workflow Management: Provides an out-of-the-box workflow covering the entire process from indexing of samples to sequencing and delivering results to clients.
• Automated Sample Assignment: Configured to automate sample assignment on plates, accommodating various plating requirements for assays and habitats.
• Streamlined Parallel Processing: Automatically segregates samples from different projects and orders as they are funneled into the Sapio Process queue.
• Pooled Sample Management: Manages pooled samples and visualizes a hierarchical, parent-child pedigree of samples and subsamples through the NGS workflow.
• Contaminant Tracking: Tracks all associated materials, reagents, and instruments used in experiments to facilitate monitoring and containment of potential contaminants.
• Automated Quality Control (QC) Decisions: Applies preconfigured rules to automatically make QC decisions, rerouting samples or rejecting them based on thresholds.

The Results: Standardized Workflows and Automated Quality Control

Comprehensive Workflow Standardization

NatureMetrics is using the Sapio platform to standardize its complex NGS workflows and remove critical data-management bottlenecks. “It was game-changing to find one out-of-the-box workflow that could cover our entire process from start to finish, including everything from indexing of samples to sequencing and delivering results to our clients,” said Dr. Briscoe.

Enhanced Sample Processing Automation

For instance, the Sapio system has been configured to automate sample assignment on plates, accommodating the various plating requirements of the many assays and habitats in the NatureMetrics product catalog. Moreover, configuration has streamlined the parallel processing of samples from different projects and orders by automatically segregating samples as they are funneled into the Sapio Process queue.

Scientists were impressed with the platform’s ability to manage pooled samples, which NatureMetrics employs to parallelize the high-throughput sequencing of samples. With the Sapio platform, scientists can visualize a hierarchical, parent-child pedigree of their samples and subsamples as they progress through the NGS workflow.

Improved Quality Control and Contamination Management

The Sapio platform also helped NatureMetrics streamline decision-making around quality-control metrics related to sensitivity. NatureMetrics requires extremely high sensitivity given the tiny amounts of DNA pulled from environmental sources. This means samples are susceptible to contamination by humans and more commonly occurring species, such as livestock and other domestic animals. The Sapio platform tracking of all associated materials, reagents, and instruments used in the experiments helps facilitate monitoring and containment of potential contaminants.

Eliminated Manual Review Bottlenecks

Prior to implementing the Sapio platform, scientists at NatureMetrics required frequent meetings to review experimental metrics and determine which samples might need to be rerun after failing quality control. The Sapio platform can apply a set of preconfigured rules to make a variety of quality-control decisions automatically, rerouting samples back through sequencing when certain thresholds are reached and rejecting samples that fail to meet specific measures. “This hard set of rigorous quality control rules is enabling us to eliminate these meetings so that we can better focus resources on processing samples through the lab,” said Dr. Briscoe.

Customer Quotes

“We developed somewhat clever methods of interlinking between spreadsheets and built dashboards to help manage processes.” – Dr. Andrew Briscoe, Science Director at NatureMetrics

“The openness and flexibility of the Sapio solution impressed us, and the low-code/no-code system has enabled us to define standard processes and, importantly, make changes as our needs and technology evolve.” – Dr. Andrew Briscoe, Science Director at NatureMetrics

“It was game-changing to find one out-of-the-box workflow that could cover our entire process from start to finish, including everything from indexing of samples to sequencing and delivering results to our clients.” – Dr. Andrew Briscoe, Science Director at NatureMetrics

“This hard set of rigorous quality control rules is enabling us to eliminate these meetings so that we can better focus resources on processing samples through the lab.” – Dr. Andrew Briscoe, Science Director at NatureMetrics

“We really tried to break the system during the UAT phase to know exactly how the system would react to different scenarios.” – Dr. Andrew Briscoe, Science Director at NatureMetrics

Lessons for NGS Labs 

NatureMetrics learned several key lessons while implementing the Sapio platform, offering insights for other organizations managing complex, high-throughput workflows:

• Prioritize a Unified, Out-of-the-Box Workflow: Seek a single solution that can cover the entire end-to-end process, from sample indexing to sequencing and result delivery, to eliminate data-management bottlenecks and fragmented systems.
• Value Openness, Flexibility, and Low-Code/No-Code Capabilities: These features enable the definition of standard processes and crucial adaptability to evolve with changing needs and technology.
• Embrace Automated Quality Control: Implement systems that can apply preconfigured rules for automated QC decisions, streamlining sample routing, reducing manual review meetings, and allowing resources to focus on core processing.
• Conduct Rigorous Testing (UAT): Thoroughly test the system, even trying to “break” it, during the User Acceptance Testing (UAT) phase to understand its behavior in different scenarios and ensure robustness.
• Ensure Detailed Documentation: Having detailed documentation of requirements and existing processes is crucial for rapid and efficient implementation.
• Adopt a Phased Rollout Strategy: Running the new system alongside old ones during rollout can facilitate training, help identify and resolve bugs, and ensure a smoother transition to live operation.
• Plan for Future Integration: Consider a platform’s ability to integrate with instrument software, ERP, and data warehouses for long-term scalability and comprehensive data management.

Next Steps

Thinking ahead, NatureMetrics will be adding additional elements currently managed on different platforms, including ways to track stock levels and equipment maintenance. Dashboards are also being implemented for different scientific tasks. In the long term, the company plans to integrate the Sapio platform directly with instrument software and other business systems, including NatureMetrics’ ERP and data warehouse.

Conclusion

NatureMetrics has successfully standardized its complex NGS workflows and transformed its data management by adopting the unified Sapio LIMS platform. This implementation has enabled end-to-end sample management and automated quality control and removed critical bottlenecks, allowing NatureMetrics to focus on its grand mission of creating a comprehensive database of life on earth to inform global sustainability and conservation efforts.

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FAQ

Q: What problem was NatureMetrics solving?
A: Bottlenecks from spreadsheet-based NGS tracking and lack of automated quality control.

Q: Why did they select Sapio LIMS?
A: For its low-code configurability, support for pooled samples, and ability to automate complex workflows.

Q: What did Sapio improve?
A: Automated plate assignment, hierarchical sample tracking, contaminant monitoring, and real-time QC decisions.

Q: What’s the strategic outcome?
A: Standardized, end-to-end NGS workflows enabling global conservation insights and future-ready data integration.