# Reconciling 16s Databases in a Single Pipeline

**URL:** https://forum.qiime2.org/t/reconciling-16s-databases-in-a-single-pipeline/31258
**Category:** Silva
**Tags:** ncbi, silva, greengenes, rdp, 16s
**Created:** [August 27, 2024, 7:25pm UTC](https://forum.qiime2.org/t/reconciling-16s-databases-in-a-single-pipeline/31258 "2024-08-27T19:25:15Z")
**Posts on this page:** 1
**Showing post:** 2

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### Author: ![SoilRotifer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/soilrotifer/32/21071_2.png) [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [August 27, 2024, 8:03pm UTC](https://forum.qiime2.org/t/reconciling-16s-databases-in-a-single-pipeline/31258/2 "2024-08-27T20:03:20Z")

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HI @pone,

I do not see why not, but it'd not be an easy task...

That being said, this is one of the many reasons why we built [RESCRIPt](https://github.com/bokulich-lab/RESCRIPt), see the paper [here](https://doi.org/10.1371/journal.pcbi.1009581). In fact, [Figure 5](https://journals.plos.org/ploscompbiol/article/figure?id=10.1371/journal.pcbi.1009581.g005) highlights the differences in taxonomic annotation that you refer to.

Each database can differ because they can make use of a different taxonomic schema, and might make different decisions about curating the data / taxonomy. I'd highly recommend reading these articles (there are more but these are a good start):

- [Microbial Taxonomy Run Amok](https://doi.org/10.1016/j.tim.2020.12.010).
- [NCBI Taxonomy: a comprehensive update on curation, resources and tools](https://doi.org/10.1093/database/baaa062).
- [Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences](https://doi.org/10.7717/peerj.4652).
- [Taxonomy annotation and guide tree errors in 16S rRNA databases](https://doi.org/10.7717/peerj.5030).

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