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This 2023 paper compared Illumina and Nanopore shotgun sequencing for identifying bacteria strains with little genomic variation between them. Both Illumina and Nanopore were able to correctly identify the bacteria strains, despite the higher error rate of the Nanopore sequences.

Reference paper

Data used in this workshop is from a paper that compared Illumina and Nanopore 16S datasets.

https://www.mdpi.com/2073-4425/11/9/1105

2.8. Sequence Data Availability

The Illumina and nanopore sequence datasets of the nose swab samples, generated and analyzed in the current study, are available in the European Nucleotide Archive (ENA) under accession number PRJEB28612

https://www.ebi.ac.uk/ena/browser/view/PRJEB28612

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