BEST LIMS FOR GENOMICS LABS

Your genomics lab runs on intelligent workflows.
Your LIMS should too.

QLIMS is purpose-built for genomics laboratories, from sample accessioning through sequencing to final report.
No spreadsheets. No generic lab software. A LIMS that actually understands NGS.

Book a demo What to look for LIMS in genomics
What is the best LIMS for a genomics lab?

The best LIMS for a genomics lab is one that handles the full next-generation sequencing (NGS) workflow natively, from sample receipt and QC through library preparation, pooling, sequencing, and results reporting, without requiring heavy customisation for each step.

It needs to integrate directly with sequencing instruments like Oxford Nanopore and Illumina platforms, enforce compliance with 21 CFR Part 11 and CAP/CLIA standards, and scale from small research labs to high-throughput clinical operations.

QLIMS was built specifically for these requirements, with pre-configured genomics workflows, instrument integration across Qubit, Tapestation, Nanodrop, NovaSeq, and ONT platforms, and a cloud-native AWS architecture that grows with your lab.

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What to look for when choosing a LIMS for genomics

Not all LIMS platforms are built for genomics. These are the capabilities that matter most when evaluating options.

NGS Workflow Coverage

The LIMS must handle library prep, pooling, demultiplexing, and flow cell management natively — not through workarounds or custom scripting. Pre-configured workflows for WGS, WES, cfDNA, ctDNA, liquid biopsy, PCR, and qPCR should ship out of the box, covering every step from sample accessioning through to sequencing run management.

Instrument Integration

Direct, bidirectional connectivity with sequencing instruments eliminates manual data transfer errors and creates a complete, unbroken chain of custody from sample to result. Look for native integrations with Oxford Nanopore (MinKNOW), Illumina NovaSeq, Agilent Tapestation, Qubit, and Nanodrop.

Sophia AI

Our smart assistant, Sophia AI, powered by Anthropic’s Claude, delivers instant insights, natural language search, and easy data retrieval. Find information fast, generate report summaries, and navigate datasets effortlessly. And more powerful features are coming soon!

Regulatory Compliance

Clinical genomics labs require 21 CFR Part 11, CAP, and CLIA support. Audit trails and electronic signatures need to be built in — enforced automatically through the workflow, not as a separate compliance layer scientists have to remember to engage.

Configurable Workflows

QLIMS provides a highly flexible, no-code environment where users can configure screens to match their workflows. Move fields, add user-defined data points, restrict inputs, and optimise interfaces—all within the platform, no programming necessary.

QC Integration

Automated QC checkpoints with configurable rules for concentration, purity, fragment size, and other genomics specific quality metrics. By automating QC processes and integrating them directly into your sequencing workflows, QLIMS minimises manual intervention and reduces the risk of errors, ensuring consistent and reliable results.

Barcode & QR Code Integration

Boost efficiency with automated data capture. With off-the-shelf integration with Bartender by Seagull Scientific, generate and scan barcodes or QR codes to reduce errors, streamline workflows, and integrate directly with label printers.

Cloud Scalability

Genomics generates enormous data volumes — terabytes per sequencing run. Cloud-native architecture ensures your LIMS scales with throughput, keeps data secure across sites, and delivers consistent uptime. Look for AWS hosting with 99.9% SLA, encrypted data transmission, role-based access control, and multi-site collaboration support.

Plate & Inventory Management

Sophisticated plate mapping, pooling, splitting and library preparation tracking designed specifically for genomics workflows. Never lose track of your reagents and consumables.

Built for the way genomics labs actually work

QLIMS covers every stage of the genomics pipeline, with pre-configured workflows for the most common sequencing applications and the flexibility to extend as your lab evolves.

Sample Management

Every sample tracked from receipt to report. DNA, RNA, cfDNA, tissue — nothing falls through the cracks.

Workflow Automation

NGS, WGS, PCR, liquid biopsy — pre-configured and running from day one. No manual steps, no bottlenecks.

Quality Control

Automated checkpoints at every stage. Bad samples get caught before they reach the sequencer.

Compliance & Reporting

21 CFR Part 11, CAP, CLIA — built in, not bolted on. Audit trails and reports generated automatically.

Connects with the instruments your lab already runs

Real-time data exchange with Oxford Nanopore sequencers, ensuring complete sample traceability through long-read sequencing runs.

Automated import of Nanodrop concentration and purity measurements directly into your QC workflow — no manual data entry.

Pulls Qubit fluorescence readings automatically into QLIMS QC checkpoints for accurate DNA and RNA quantification tracking.

Seamless integration with Hamilton liquid handling systems for automated sample preparation and pipetting workflows.

Direct connectivity with Illumina’s high-throughput sequencing platform, supporting sample sheet generation and run tracking.

Bi-directional integration with hospital and clinical information systems for seamless patient data exchange and reporting.

Industry-standard healthcare data exchange protocols for clinical lab interoperability and electronic health record connectivity.

Automated import of fragment size and integrity data from Tapestation runs directly into QLIMS QC steps.

Data migration and interoperability support for labs transitioning from or running alongside Clarity LIMS environments.

Integration with Beckman Biomek liquid handling robots for high-throughput automated sample processing.

Connect sequencing outputs to Basepair’s bioinformatics platform for streamlined analysis pipeline management.

"We can tell you that without QLIMS thaere’s no way we could cope with a thousand samples in a year. If somebody from another lab asked me, ‘Would you recommend QLIMS?’ I’d say, if it’s to try and replicate similar things to what we’ve done, absolutely, hand on heart, these guys will sort you out."
OnQ Software - LIMS For Genomics Labs

Built for every type of genomics lab

From high-throughput sequencing cores to clinical diagnostics and agricultural genomics,
QLIMS adapts to the workflow — not the other way around.

Research Genomics

  • Project-based sample organisation
  • Multi-institutional collaboration tools
  • Long-term sample storage and retrieval
  • Scalable pricing for growing teams

Clinical Genomics

  • Clinical variant interpretation workflow
  • EMR and clinical decision support integration
  • Automated clinical report generation
  • Granular security and access control

High-Throughput Sequencing

  • Automated batch processing at scale
  • Advanced pooling and demultiplexing
  • Parallel workflow execution
  • Automated failure handling

Agriculture & Environmental

  • Field sample collection with GPS integration
  • Environmental monitoring and compliance
  • Crop and livestock genomics workflows
  • Remote Sampler integration

QLIMS vs other genomics LIMS platforms

A practical comparison of the most common genomics LIMS options across the criteria that matter most to sequencing labs.

Capability QLIMS Illumina-Native LIMS R&D Focused LIMS No-Code LIMS
Pre-configured NGS workflows ✓ ✓ Single platform only Partial Partial
Oxford Nanopore Compatible Product ✓ ✗ ✗ ✗
Cloud-native (AWS) ✓ On-premise option ✓ ✓
Enterprise-grade cloud security (AWS Qualified) ✓ ✗ ✗ ✗
Multi-platform instrument support ✓ Single vendor only ✓ ✓
21 CFR Part 11 compliance ✓ ✓ Partial ✓
CAP / CLIA accreditation support ✓ Partial ✗ Partial
No-code workflow configuration ✓ ✗ Limited ✓
Robotic integration ✓ ✓ ✗ ✗
Statistical QC charting (Levey-Jennings) ✓ Limited ✗ Limited
Multi-site collaboration ✓ Limited ✓ ✓
Common questions about LIMS
for genomics labs
QLIMS is purpose-built for NGS workflows — covering every step from sample accessioning through sequencing to final report, with pre-configured workflows for WGS, WES, cfDNA, and liquid biopsy out of the box. It integrates directly with Oxford Nanopore, Illumina NovaSeq, Qubit, Tapestation, and Nanodrop, eliminating manual data transfer at every handoff. Compliance is built in from day one — 21 CFR Part 11, CAP, and CLIA — not added as an afterthought. And as an AWS-native SaaS platform, it scales with your throughput without infrastructure overhead. For NGS labs that need a LIMS that actually understands sequencing, QLIMS is the answer.
Yes. QLIMS integrates directly with MinKNOW from Oxford Nanopore Technologies and is a member of the Oxford Nanopore Compatible Products Programme. This enables real-time data exchange between the sequencer and QLIMS, eliminating manual data transfer and ensuring complete traceability through the long-read sequencing workflow.
Yes. QLIMS supports 21 CFR Part 11 compliance through electronic signatures, audit trails, version control, and role-based access. It also supports CAP and CLIA requirements for clinical genomics environments.
QLIMS uses a genomics-optimised implementation approach that significantly reduces deployment time. With pre-configured workflows for NGS, WGS, WES, PCR, and liquid biopsy, most labs focus on configuration rather than building from scratch. Some customers, like the Garvan Institute of Medical Research, achieved up to 75% out-of-the-box coverage.
QLIMS supports WGS, WES, targeted panels, cfDNA/ctDNA, liquid biopsy, PCR, qPCR, and amplicon sequencing. It covers the full workflow from sample receipt through QC, library prep, pooling, and sequencing run management.
Yes. QLIMS supports both research and clinical environments. Research labs benefit from flexible project-based organisation, while clinical labs use compliance features, EMR integration, and structured reporting workflows.
Yes. QLIMS is built for scalability with batch processing, parallel workflows, robotic integration (Hamilton, Biomek), and AWS cloud infrastructure supporting high-volume sequencing operations with high uptime and performance.

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Book a personalised demo with our genomics team. We’ll walk through your specific workflows
and show you exactly how QLIMS fits.

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