A comprehensive matched cDNA and direct RNA dataset of UHRR and HG002
June 29, 2026
2 min
ZymoBIOMICS Fecal Reference metagenomic WGS
Overview
We are pleased to announce the release of an updated ZymoBIOMICS Fecal Reference dataset to highlight the capabilities of Oxford Nanopore Technologies’ for metagenomic analysis. This release includes: new basecalls (including 6mA, 4mC, and 5mC modified basecalls) for the PromethION Flow Cell data previously released in our LC2024 data release; an additional PromethION Flow Cell of sequencing data from the same sample; and new analysis results highlighted in our Metagenomics Application Note.
Dataset
The dataset is available for anonymous download, without login, from a public Amazon Web Services S3 bucket. The bucket is part of the Open Data on AWS project enabling sharing and analysis of a wide range of data. The data can be downloaded with the AWS CLI command:
aws s3 sync --no-sign-request s3://ont-open-data/zymo_fecal_2025.05 zymo_fecal_2025.05
See the tutorials page for information on downloading the dataset. You can also browse and download the files in your web browser courtesy of 42basepairs.
| Folder name | Size | Description |
|---|---|---|
| RAW | 4.6 TB | POD5/Flowcell files |
| Basecalls | 850 GB | BAM files |
| Analysis | 1.2 TB | Analysis outputs |
Sample
| Attribute | Value |
|---|---|
| Sample Name | ZymoBIOMIC D6323 |
| Organism | metagenomic community |
| Molecule Type | gDNA |
| Sample Type | inactivated cultured stool |
| Biological replicates | 2 |
| Flow Cell replicates | 1 |
| Link to sample source | ZymoBIOMICS Fecal Reference with TruMatrix Technology |
Preparation
Sample preparation was performed according to protocols published on the main Oxford Nanopore Technologies’ website.
| Attribute | Value |
|---|---|
| Extraction | QIAamp PowerFecal DNA Kit |
| Library Prep | Ligation sequencing kit (LSK114) |
| Kit | LSK114 |
Further preparation information such as sample storage suggestions can be found on the Oxford Nanopore website.
Sequencing
Sequence data was generated using the following configuration:
| Attribute | Value |
|---|---|
| Flow Cell | FLO-PRO114M |
| Device | PromethION |
| Chemistry | R10.4.1 |
| Basecall Model | 5.0.0 |
| MinKNOW Version | 5.9.7 |
| Modified bases | 4mC_5mC, 6mA |
Analysis
Analysis outputs are available. The analysis results are located in the S3 bucket under the prefix:
s3://ont-open-data/zymo_fecal_2025.05/analysis
The analysis results include metagenomic assembly contigs from MetaMDBG, metagenome binning results from SemiBin2 and MetaBAT2, consensus metagenome bins from DAS Tool, and quality metrics from CheckM2. We also include a script containing all the commands used to generate these analysis results. For further information on the analysis see the linked Applications Note.
Other software used for analysis:
| Tool | Version |
|---|---|
| Dorado | v0.9.1 (HAC) |
| Dorado | v0.7.3 (SUP) |
| MetaMDBG | v1.0 |
| SemiBin2 | v2.1.0 |
| MetaBAT2 | v2.17 |
| DAS Tool | v1.1.7 |
| CheckM2 | v1.0.2 |
| Minimap2 | v2.28 |
Related Materials
- Oxford Nanopore Technologies’ provides superior metagenome-assembled genome recovery and strain-level resolution from a complex microbiome Applications Note
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Sean McKenzie
Bioinformatician
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