Agilent SLIMS for Next Generation Sequencing

Integrate and streamline your NGS workflows


Track and trace NGS data and workflows with ease

Why continue to struggle with information overload when there is a simple solution? SLIMS is a single system that lets you take control of all your lab information and save time, money, and morale. SLIMS is easier and faster to deploy than a traditional LIMS (laboratory information management system), so you can get proactive about integrating, automating, and visualizing your entire sample management process. And the sooner you adopt SLIMS, the greater the benefits—now and over time.

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SLIMS advantages for NGS

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Connect your NGS instruments
Streamline compliance with HIPAA, CLIA, CAP and more
Automate metadata recording and reporting
Visually track massive volumes of sample data
Organize boundless tasks
Manage access rights easily
End-to-end sample management

SLIMS for NGS combines the best of a LIMS and NGS workflow management capabilities. Point-and-click automation facilitates the entire pipeline, instructing the user what to do—from order creation to variant analysis—with integration from Agilent Alissa Interpret. Now you can manage samples from one stage to another, track location and assignment, receive guidance for complex workflows, review by exception, and facilitate collaboration without creating delays. SLIMS is also exceptionally adaptable, so it is easy to configure to match your lab’s unique processes.

SLIMS allows lab staff to track every step of the sample management process and find paths to all relevant content. It provides:

  • Tracking from receipt to storage and delivery
  • Chain of custody tracking of all locations at all times
  • Flexible metadata for samples
  • Usage tracking and stock management for standards and reagents
  • Derivations, aliquoting, and mixing (pooling)
  • Printing of custom labels and barcodes to make it easy to find anything in the lab
Flexibility through integration and automation

With SLIMS for NGS, one automated system supports your entire NGS workflow. Using the SLIMS Store module, just click to download a configuration, quickly and easily integrating your samples, plates, assays, and instruments. Index plates can be downloaded and re-configured in any order. Simply choose your kit and SLIMS installs the workflow, reagents, and adapter barcodes!

Index sets from major providers
SLIMS provides index sets for Agilent SureSelect, Illumina Nextera XT, BGI, and 10x Genomics, and more. Uploading a custom set is easy and can be done through Excel. Let SLIMS suggest the adapter plate to apply to your sample plate in the workflow.


Index sets from major providers

  • Seamlessly integrate with your EMR (electronic medical record) using easy SLIMS plugins that are designed
  • Download our plugins from the SLIMS Store to generate sample sheets and import results from NGS QC
  • Use our core sequencing workflows to integrate with sequencing instruments, Illumina BaseSpace.
  • Use the SLIMS API to connect seamlessly with your own data pipeline.

Workflow automation
SLIMS makes it easy to automate previously manual processes to increase efficiency and reduce errors, you can add new requests to samples from workflow, automate the addition of control samples, and apply rules to validate pools and storage. Just point and click to add a wide range of protocols like DNA/RNA extraction, library preparation, QC, normalization, pooling, and sequencing.

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Visibility into the entire workflow

SLIMS is visual, intuitive, and easy to use. It gives you a graphical, up-to-date view of the entire workstream or any part of it, so users can always see what’s happening and what’s next on their to-do list. No more sorting through data and tasks that aren’t relevant to them.

With the graphical interface, it is simple to create and filter content. Users can customize which content to display, see all sample attributes—such as unique identifier, content type, and status—modify attributes, and see any changes from the original content, including who made the change and date and time of the change, in a way that helps you meet your 21 CFR part 11 compliance obligations. For example, you can see immediately how many samples are in process within a certain protocol type. By clicking on any item, you are directly routed to the corresponding protocols so you can start or continue your work or review what has been done. Just open SLIMS to start your work or review your tasks.

Reliable and scalable data management

SLIMS for NGS is a one-stop-shop for data. It consolidates your samples and data in one place. It makes data instantly accessible to authorized lab personnel and managers, even remotely—in multiple time zones and for multi-site labs. SLIMS architecture scales to meet the requirements of data-intensive or complex workflows. You always have the storage space you need and the ability to reliably organize what you collect. And by doing so digitally and automatically, you produce results that are more consistent, higher in quality, and easier to audit.

Instantly operational

SLIMS for NGS offers flexible installation options. It can be hosted by Agilent on a scalable, powerful, secure server, or by your favorite cloud service provider. The system can also be installed on a server within your IT infrastructure. SLIMS for NGS runs on a web browser, requires no further software on client computers, and can also be used on tablets.

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Faster results

Your lab’s workflow accelerates because the process is automated and transparent, and you can see business results sooner because the implementation process for SLIMS for NGS is rapid. For example, if you need to extract DNA and run an Agilent SureSelect XT kit on a Novaseq, you can deploy the default workflow in minutes.

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Agilent SLIMS engineers are domain experts with backgrounds in science and laboratory informatics. We have deployed solutions for labs in more than 20 countries. We support you in all the phases of the project, from installation and configuration to validation and ongoing assistance.

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The SLIMS Store gives you access to pre-configured tools for rapid implementation. Choose from a library of sample types, locations, metadata, automation snippets, and many more to make your solution operational as fast as possible. Install what you need and use it as is or adapt it to make SLIMS ready for your lab.

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Case Study

Read how this customer is using Agilent SLIMS to improve efficiency and move his research forward..

Download it here!
case study

On-Demand Webinars

Learn the basics of the Agilent SLIMS Lab Workflow Platform

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What our clients say

Hear what our clients have to say about their experience with SLIMS

king college london

“SLIMS brings together different management systems for reagents, antibodies, mice, everything... all in a single system. There's a depth and a richness to what's being captured that didn't exist before.”

logo aalborg university hospital

“SLIMS' features support our Hospital by helping to track and trace samples coming from different hospitals, linking subjects to samples, protocols, and results. It enables registering, scheduling, and validating of orders. The ELN module allows tracking of sequencing runs with a live overview, together with a wide range of information required by the scientists and guides in the workflows for NGS assays with an easy to follow, step-by-step protocol. In addition, it shows a live overview of samples and orders’ statuses containing every data linked to a specified sample and to its derivative”

Frequently Asked Questions

Next-generation sequencing (NGS) refers to high-throughput, massively parallel sequencing technologies for studying genetic variation associated with disease or other biological research. NGS improves upon chain termination sequencing, or Sanger sequencing, which revolutionized biological research, allowing researchers to determine genome sequences for the first time.

The primary difference between NGS and first-generation sequencing is throughput. NGS offers parallel sequencing of millions of small fragments of DNA per run. With conventional sequencing, or Sanger sequencing, only a few bases can be decoded per reaction using a time-consuming analysis. To give an example of the volume and throughput improvements, NGS can sequence an entire human genome in a single day, while the Sanger sequencing method that was used to decider the first human genome took more than a decade to decode. The massive improvement in throughput for NGS also led to a dramatic decrease in DNA sequencing costs.

All laboratory information management systems (LIMS) for NGS allow users to manage samples and associated data more easily and effectively. For any NGS workflow, a good LIMS can:

  • Streamline compliance with HIPAA, CLIA, CAP, and other standards
  • Visually track massive volumes of sample data
  • Connect your NGS instruments
  • Eliminate the need to search for slow and disconnected Excel data
  • Automate metadata recording and reporting
  • Organize boundless tasks
  • Manage variant analysis for tertiary analysis

NGS is a complex scientific process that covers many steps, with QC checks along the way to ensure high-quality, consistent data. These steps include:

  • Sample collection
  • Sample preparation
  • Library preparation
  • Target enrichment
  • Sequencing
  • Data analysis and reporting
full ngs workflow

LIMS can connect all the instruments and software packages that are used across your NGS workflow, from liquid handlers to instrumentation to NGS data analysis software. For the sequencers specifically, the instrument generates a massive amount of NGS data, which gets stored and analyzed. The LIMS then finds the key results and presents them in a report.

There are a few common challenges that NGS laboratories face, many of which can be prevented by an Agilent product or solution.

  • Challenge: Storing data in a reusable way. Solution: Agilent SLIMS is beneficial for searching and creating links between samples, procedures, and sample results, compared to common spreadsheet systems, such as Microsoft Excel. While Excel is easy to use and versatile, it is less desirable for retrieving information or structuring information.
  • Challenge: Ensuring the sample quality is always up to certain level. Solution: Routine QC checks can ensure sample quality. Integrated and automated sample QC is ideal for efficiency and ease of use in an NGS workflow, as is the case with Agilent TapeStation systems fully integrated with Agilent SLIMS.
  • Challenge: Library preparation is complex and error prone. Solution: Agilent SLIMS provides intuitive controls and user guidance to set up protocols more easily and quickly, while automation can reduce contamination, errors, and costs per sample. The Agilent Bravo is a flexible liquid handling platform that can automate your NGS sample preparation, freeing up time while generating consistent data.

To assure compliance, an NGS lab should meet the following standards, including: HIPAA, CLIA, ISO 13485, ISO/IEC 17025, and ISO 15189.

NGS is a strategy that is used to test many genes simultaneously to determine the order of nucleotides in entire genomes or targeted regions of DNA or RNA. NGS can be used to detect variants or mutations. For example, in cancer, NGS can be applied to a patient’s tumor that has been biopsied or removed.

Real-time polymerase chain reaction (PCR) is an easier and more forgiving technique with limited ability to multiplex. NGS allows analysts to simultaneously determine many gene sequences while revealing exact changes. However, NGS is a more technically demanding and costly process than PCR.

Quantitative polymerase chain reaction (qPCR) works best for low-throughput laboratories with low target numbers. NGS is more scalable and better suited for high-throughput sequencing, and it offers higher discovery power and higher sensitivity.

Decades after the invention of sequencing DNA, more than 10,000 NGS systems are installed globally. With next-generation sequencing now accepted as current-generation sequencing, labs are now facing the challenge to provide higher throughput and get more organized. Regulatory bodies also play a role, as they require laboratories to record more data and be fitted for long-term tenures. As such, there is a need for implementing a digital solution to manage the entire NGS workflow with consistency, while focusing on productivity.

With SLIMS, in addition to a broad NGS portfolio, Agilent provides a comprehensive software solution that manages and tracks all samples over the laboratory workflow. This includes quality control measures to be taken during sample collection, before sample use, NGS library QC, and during target enrichment. SLIMS also provides the sophisticated controls needed to ensure that data remain securely sorted and accessible for years to come.

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