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. 2023 Apr 20;3:33. doi: 10.1038/s43705-023-00239-3

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Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — The preprocessing script contains quality control steps that remove primers and filter sequences outside the specified length parameters. The Stream 1 workflow uses the assignTaxonomy function from dada2 to assign taxonomy to all Nanopore sequences. The Stream 2 workflow performs a BLASTn search of the Nanopore sequences as queries against a custom database.