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DNA Metabolomics
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Long-Read Sequencing

In addition to the Illumina short-read sequencers, the Core Facility offers access to two Oxford Nanopore long-read sequencers, the GridION and PromethION 2 Solo (P2S). Nanopore sequencing with Oxford Nanopore Technologies (ONT) systems enables high-throughput long-read sequencing of DNA and RNA samples, including genomic DNA, amplified DNA, cDNA and RNA. Read lengths with an average of 10,000 to >100,000 bases are possible. DNA or RNA can also be sequenced directly without prior amplification or reverse transcription, allowing direct detection of epigenetic base modifications.

More information can be found at: https://nanoporetech.com/platform/

In addition to the Illumina short-read sequencers, the Core Facility offers access to two Oxford Nanopore long-read sequencers, the GridION and PromethION 2 Solo (P2S). Nanopore sequencing with Oxford Nanopore Technologies (ONT) systems enables high-throughput long-read sequencing of DNA and RNA samples, including genomic DNA, amplified DNA, cDNA and RNA. Read lengths with an average of 10,000 to >100,000 bases are possible. DNA or RNA can also be sequenced directly without prior amplification or reverse transcription, allowing direct detection of epigenetic base modifications.

More information can be found at: https://nanoporetech.com/platform/

Long-Read Sequencing Overview

Oxford Nanopore offers several different library preparation kits for DNA (see: https://nanoporetech.com/products/prepare/dna-library-preparation) or for RNA (see: https://nanoporetech.com/products/prepare/rna-library-preparation) that can be used in the Core Facility.

However, due to the wide variety of protocols, it is essential to discuss a project with us in advance to determine if library preparation can be offered for your specific project.

The GridION can operate up to five MinION flow cells in parallel. Typically, 10 to 20 Gb of data can be expected per flow cell. This makes the system well suited for applications such as metagenomics, targeted sequencing or small transcriptomes where 10 to 100 Gb of data is sufficient.

We offer the following options for sequencing on GridION, from full service to pure self-service:

  • Sequencing plus library preparation using standard Oxford Nanopore kits, e.g. Ligation Sequencing Kit
  • Sequencing of customer libraries (The Core orders the flow cells and carries out the sequencing.)
  • Sequencing only service (The customer delivers flow cell(s) and the library, and the Core carries out the sequencing.)
  • Sequencing self-service (A trained user runs GridION independently to sequence their own library. Flow cell and reagents are provided by the user.)

The P2S can operate up to two PromethION flow cells in parallel. Typically, 90 to 100 Gb of data can be expected per flow cell. In contrast to the GridION, the system is therefore also suitable for sequencing large genomes and transcriptomes or a larger number of samples on one flow cell by barcoding individual samples.

We offer the following options for sequencing on P2S, from full service to pure self-service:

  • Sequencing plus library preparation using standard Oxford Nanopore kits, e.g. Ligation Sequencing Kit
  • Sequencing of customer libraries (The Core orders the flow cells and carries out the sequencing.)
  • Sequencing only service (The customer delivers flow cell(s) and the library, and the Core carries out the sequencing.)
  • Sequencing self-service (A trained customer runs P2S independently to sequence their own library. Flow cell and reagents are provided by the customer.)

The customer will receive a link to download the raw data (.POD5 files) and the sequencing data (.FASTQ files). Basecalling can be done with three different models: a Fast model, a High accuracy (HAC) model and a Super accurate (SUP) model. Aligned reads (.BAM files) are also available if the user provides an alignment reference file as a .fasta or .mmi file.

Instruments run by Core Staff and trained users:

  • GridION
  • PromethION 2 Solo (P2S)

Users can access our instruments for self-service use after prior training by facility staff. Please contact us to arrange training.

Our Contact

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Core Facility Genomics

Ingolstädter Landstraße 1 85764 Neuherberg, Building 34 & 35.37