Sample datasets
What we'll actually work with
This training follows one sample end to end, from raw reads through to annotation: the ERR* samples from a real hospital genomic surveillance study (below), which map directly onto this training's own outbreak scenario. For the QC and preprocessing modules specifically, we'll also work hands-on with two additional, unrelated example datasets — barcode01 and PBK97200 — chosen for their contrasting quality profiles.
The ERR* samples: a hospital carbapenemase surveillance study
The ERR* samples come from a retrospective analysis of carbapenemase-producing Gram-negative bacteria isolated at Cambridge University Hospitals NHS Foundation Trust (CUH) in the UK between 2014 and 2020 (n=165).
barcode01 and PBK97200: the QC/preprocessing examples
barcode01 comes from a separate study demonstrating ONT-based finishing of bacterial genomes: 12 Klebsiella pneumoniae isolates multiplexed and sequenced together on a single MinION flow cell, then assembled using a combination of ONT long reads and pre-existing Illumina short reads.
PBK97200 comes from a benchmarking dataset built to test a bacterial genome workflow's reproducibility: 24 isolates spanning 15 species (across genera including Bacillus, Klebsiella, Salmonella, and Staphylococcus), each run in quadruplicate on a single PromethION flow cell.
How each dataset was generated
| ERR* samples | barcode01 | PBK97200 | |
|---|---|---|---|
| Device | MinION | MinION Mk1B | PromethION 2 Integrated (P2i) |
| Flow cell / chemistry | R9.4.1 | FLO-MIN106, R9.4 | FLO-PRO114M, R10.4.1 |
| Library / barcoding kit | SQK-RBK004 rapid barcoding | SQK-LSK108 ligation kit | SQK-RBK114.96 Rapid Barcoding Kit 96 V14 |
| Basecaller | Guppy v3.6.0, high-accuracy model | Albacore v1.1.2 | SUP@5.2.0 model (MinKNOW v25.11.0) |
References
Roberts LW, Enoch DA, Khokhar F, et al. Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years. Microbial Genomics. 2023;9(7):mgen001048. doi:10.1099/MGEN.0.001048
Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microbial Genomics. 2017;3(10):e000132. doi:10.1099/MGEN.0.000132/CITE/REFWORKS
NO-MISS Bacterial isolate dataset | EPI2ME Blog. Accessed September 16, 2026. https://epi2me.nanoporetech.com/nomiss_96bc_p2i_sup_2026/