Questions about denoising-CCS with Dada2

Citation for denoising-CCS in Dada2. Hi Qiime2 team, since the Dada2 PacBio CCS denoising method was also added in this release but the dada2 --citation only cites the original short reads version of dada2 (I installed via bioconda channel). I am wondering whether it is also useful to cite the Dada2 PacBio-CCS paper, which is published in 2019 in NAR: https://academic.oup.com/nar/article/47/18/e103/5527971. Best, Jianshu

Hi all, just wondering what the new error model will be (is there a paper related to this model?) used for Dada2 since it is the initial error model and did not change since then. Best, Jianshu

Hello @jianshu93

Welcome to the forums! :qiime2:

Yes, you could cite both the original DADA2 paper (PMC4927377) and the CCS followup paper (PMC6765137).

Error models depend on sequencing method, which is why the current plugin has methods for Illumina single, Illumina paired, Pyrosequencing, and PacBio CCS.
https://docs.qiime2.org/2024.10/plugins/available/dada2/

The Qiime2 plugin for DADA2 PacBio CCS was added back in 2022, so I feel I may be misunderstanding your question...

Let me know if that helps!

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Yes for sure. I mean qiime dada2 --citation command only reported the first paper only but not the CCS paper. Just think it should also be added there. Jianshu

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Hey @jianshu93,

Thanks for bringing that up as a suggestion, you're totally right - I've opened up a PR that adds this citation to q2-dada2, so you'll see this change reflected in the next QIIME 2 release (2025.4).

Cheers :lizard:

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