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Merge pull request #1852 from leholman/patch-1
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new PR2 database levels
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benjjneb authored Nov 14, 2023
2 parents 59be812 + 352da05 commit edbe9f8
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4 changes: 2 additions & 2 deletions training.Rmd
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Expand Up @@ -47,9 +47,9 @@ We maintain reference fastas for the three most common 16S databases: Silva, RDP

* [nifH ARB, version 1](https://doi.org/10.5281/zenodo.3958364)

* [PR2 version 4.7.2+](https://github.com/vaulot/pr2_database/releases). SEE NOTE BELOW.
* [PR2 version 5.0.0+](https://github.com/vaulot/pr2_database/releases). SEE NOTE BELOW.

**Note:** PR2 has different `taxLevels` than the dada2 default. When assigning taxonomy against PR2, use the following: `assignTaxonomy(..., taxLevels = c("Kingdom","Supergroup","Division","Class","Order","Family","Genus","Species"))`
**Note:** PR2 has different `taxLevels` than the dada2 default. When assigning taxonomy against PR2, use the following: `assignTaxonomy(..., taxLevels = c("Domain","Supergroup","Division","Subdivision","Class","Order","Family","Genus","Species"))`


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