Long Read Sequencing
Meet Our Experts
Project Management
Protocol Benchmarking
Optimisation and Troubleshooting
Novel Protocol Development
Sample and Library Prep
Sequencing and Run QC
Protocol Benchmarking
Optimisation and Troubleshooting
Novel Protocol Development and Implementation
Sample and Library Prep
Sequencing and Run QC
Protocol Benchmarking
Optimisation and Implementation
Analysis Consulting
Analysis Implementation
Benchmmarking and Troubleshooting
Data Transfer and Security
Pipeline Operations
Hardware, Software, Firmware Upkeep
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Long Read (ONT) Sequencing: About us
Nanopore sequencing is a disruptive maturing technology, which has been readily adopted in life sciences. It allows the sequencing of long, native stretches of DNA and RNA and provides a completely new view of the genome and transcriptome.
Long Read Sequencing Expertise Unit supports native and PCR, DNA and RNA, Whole or Targeted, Genome and Transcriptome Long Read sequencing applications using Oxford Nanopore Technologies (ONT) platforms.
We collaborate and support a variety of Nanopore Sequencing Projects with researchers and scientists from academia (beyond VIB and UAntwerp) industry and commercial entities.
Since 2015, we have been developing unique, extensive expertise and pioneering long-read sequencing using ONT platforms. Our extensive ONT expertise offers flexible nanopore sequencing solutions at a cost-effective price.
*NEW* Affordable Plasmid sequencing using rapid prep solution* - Bored of Sanger? Try Nanopore plasmid sequencing!
Interested in methylation analysis? - Nanopore sequencing using a native approach retains methylation information
Interested in novel isoforms - It is time to try direct RNA or cDNA sequencing.
We accept NEW projects! Contact us!
Nanopore Sequencing, developed by Oxford Nanopore, is a new generation of DNA/RNA sequencing technology. It is the only sequencing technology that offers real-time analysis, which can analyze native DNA or RNA and sequence any length of fragment to achieve short to ultra-long read lengths. Small formats such as Flongle and MinION address the need for on-demand, rapid, smaller tests or experiments. PromethION 24 is the largest format for nanopore sequencing, designed to offer on-demand use of up to 24 (48) Flow Cells, and is often used in population-scale sequencing projects or any type of sequencing projects demanding higher yields.
Every sequencing project starts with an extensive sample QC.
While we can offer support in DNA/RNA extraction, for most projects, our work starts with extracted DNA, polyA enriched RNA, cDNA or PCR amplified (tagged), or otherwise selected fragments. We can consult on extraction methods most suitable for reliable results using Nanopore Sequencing and can offer a limited portfolio of extraction methods for mammalian (cell lines or tissue extracts) for small to mid-size projects.
LRS Expert Unit can rigorously evaluate any DNA/RNA sample and predict sequencing outcomes based on sample's purity, integrity, type, and amount.
We are using UV/VIS Spectroscopy (DropSense, Little Lunatic), Fluorescence (Qubit), and Parallel Capillary gel electrophoresis (Fragment Analyzer) to ensure samples will deliver good sequencing results. After QC, samples are prepared for library construction. Samples can be fragmented (Megaruptor3) and/or size selected (Size Selective Precipitation), depending on the needs of the project.
We have experience with various sample types:
- DNA/RNA (long or short fragments), including cfDNA.
- DNA from Prokaryotes and Eukaryotes, including DNA extracted from biofilms, bacteria, various plants, mammalian, and non-mammalian organisms.
- We are one of the sequencing collaborators in the ERGA pilot project (collaborating with UAntwerp) and were the first to publish a human DNA sequence obtained on the PromethION (collaborating with VIB TechWatch and VIB CMN) and are responsible for numerous different ONT sequencing projects for UA, VIB, and external collaborators.
After the final QC of the prepared sample, the libraries are constructed and sequenced.
While we are mostly using the PromethION platform, we do support projects using PromethION, MinION, and Flongle Flow Cells (R9.4.1 and R10.4.1).
Types of library prep protocols we offer and have experience with: Rapid Sequencing, Plasmid Sequencing, Ligation Sequencing, PCR- cDNA, Direct cDNA, and Direct RNA (with or without barcoding).
Type of projects we have experience with Whole genome (including cfDNA, plasmid, FFPE), whole transcriptome (RNA and cDNA) and targeted approaches (Selective sequencing = 'Read Until', hybridization capture, (multiplex) PCR targeted, Cas9 Capture).
For most ONT sequencing projects, we first request a (short) meeting to understand the needs of the collaborators and make sure the expectations are being managed and met. After we understand the needs of collaborators or clients, we can prepare a service agreement and cost estimation.
We also offer a limited analysis portfolio as we have developed pipelines for structural variant and single nucleotide variant analysis and methylation calling.
Sequencing data is delivered digitally using a secured link and can consist of the base called raw, annotated, or/and fully analyzed data.
Currently, we are building pipelines for plasmid analysis and primary RNA analysis, but we also help with other analyses when possible.
Contact us if you think of using ONT for sequencing! Let us connect!
We are accepting exciting new projects and would love to share our experience with ONT technology and our awareness of it!
Most recent novel applications (in development) are 10X single-cell long read sequencing, plasmid sequencing, hybridisation targeted approaches, and other RNA solutions.
Our expertise unit is also part of the CMN Neuromics Support Facility and UAntwerp Core Facility.
