Merge pull request #688 from d4straub/update-docs-tax-databases

Update docs, citations and usage with new taxonomic reference databases

CHANGELOG.md

@@ -19,11 +19,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#672](https://github.com/nf-core/ampliseq/pull/672) - Update output docs for collapsed abundance tables
-- [#673](https://github.com/nf-core/ampliseq/pull/673) - Fix logic relating to generation of qiime2 taxonomy part of summary report
+- [#672](https://github.com/nf-core/ampliseq/pull/672),[#688](https://github.com/nf-core/ampliseq/pull/688) - Updated documentation
 - [#676](https://github.com/nf-core/ampliseq/pull/676) - Phyloseq sometimes only produced one of multiple output files
 - [#679](https://github.com/nf-core/ampliseq/pull/679) - Prevent masking low complexity regions by VSEARCH with lower case letters
-- [#680](https://github.com/nf-core/ampliseq/pull/680) - Improved pipeline summary report & error messages
+- [#680](https://github.com/nf-core/ampliseq/pull/680),[#673](https://github.com/nf-core/ampliseq/pull/673) - Improved pipeline summary report & error messages
 - [#683](https://github.com/nf-core/ampliseq/pull/683) - Template update for nf-core/tools version 2.11
 - [#687](https://github.com/nf-core/ampliseq/pull/687) - Correct conda package for ASV SSU filtering
 

CITATIONS.md

@@ -41,6 +41,10 @@
 
   > Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6. doi: 10.1093/nar/gks1219. Epub 2012 Nov 28. PMID: 23193283; PMCID: PMC3531112.
 
+- [Greengenes2](https://doi.org/10.1038/s41587-023-01845-1)
+
+  > McDonald, D., Jiang, Y., Balaban, M. et al. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01845-1
+
 - [PR2 - Protist Reference Ribosomal Database](https://pubmed.ncbi.nlm.nih.gov/23193267/)
 
   > Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, Boutte C, Burgaud G, de Vargas C, Decelle J, Del Campo J, Dolan JR, Dunthorn M, Edvardsen B, Holzmann M, Kooistra WH, Lara E, Le Bescot N, Logares R, Mahé F, Massana R, Montresor M, Morard R, Not F, Pawlowski J, Probert I, Sauvadet AL, Siano R, Stoeck T, Vaulot D, Zimmermann P, Christen R. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 2013 Jan;41(Database issue):D597-604. doi: 10.1093/nar/gks1160. Epub 2012 Nov 27. PMID: 23193267; PMCID: PMC3531120.
@@ -61,13 +65,21 @@
 
   > Kõljalg U, Larsson KH, Abarenkov K, Nilsson RH, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T, Sen R, Taylor AF, Tedersoo L, Vrålstad T, Ursing BM. UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol. 2005 Jun;166(3):1063-8. doi: 10.1111/j.1469-8137.2005.01376.x. PMID: 15869663.
 
-  - [MIDORI2 - a collection of reference databases](https://doi.org/10.1002/edn3.303/)
+- [MIDORI2 - a collection of reference databases](https://doi.org/10.1002/edn3.303/)
+
+  > Leray, M., Knowlton, N., & Machida, R. J. (2022). MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences. Environmental DNA, 4, 894– 907. doi: https://doi.org/10.1002/edn3.303.
+
+- [COIDB - CO1 Taxonomy Database](https://doi.org/10.17044/scilifelab.20514192.v2)
+
+  > Sundh J, Manoharan L, Iwaszkiewicz-Eggebrecht E, Miraldo A, Andersson A, Ronquist F. COI reference sequences from BOLD DB. doi: https://doi.org/10.17044/scilifelab.20514192.v2.
+
+- [PhytoRef plastid 16S rRNA database for photosynthetic eukaryotes](https://pubmed.ncbi.nlm.nih.gov/25740460/)
 
-    > Leray, M., Knowlton, N., & Machida, R. J. (2022). MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences. Environmental DNA, 4, 894– 907. https://doi.org/10.1002/edn3.303.
+  > Decelle J, Romac S, Stern RF, Bendif el M, Zingone A, Audic S, Guiry MD, Guillou L, Tessier D, Le Gall F, Gourvil P, Dos Santos AL, Probert I, Vaulot D, de Vargas C, Christen R. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy. Mol Ecol Resour. 2015 Nov;15(6):1435-45. doi: 10.1111/1755-0998.12401. Epub 2015 Apr 6. PMID: 25740460.
 
-  - [COIDB - CO1 Taxonomy Database](https://doi.org/10.17044/scilifelab.20514192.v2)
+- [Zehr lab nifH database](http://doi.org/10.5281/zenodo.7996213)
 
-    > Sundh J, Manoharan L, Iwaszkiewicz-Eggebrecht E, Miraldo A, Andersson A, Ronquist F. COI reference sequences from BOLD DB. doi: https://doi.org/10.17044/scilifelab.20514192.v2.
+  > M. A. Moynihan & C. Furbo Reeder 2023. nifHdada2 GitHub repository, v2.0.5. Zenodo. doi: http://doi.org/10.5281/zenodo.7996213
 
 ### Phylogenetic placement
 

docs/usage.md

@@ -231,6 +231,8 @@ Pre-configured reference taxonomy databases are:
 | unite-alleuk | +     | +      | -       | +      | eukaryotic nuclear ribosomal ITS region       |
 | coidb        | +     | +      | -       | -      | eukaryotic Cytochrome Oxidase I (COI)         |
 | midori2-co1  | +     | -      | -       | -      | eukaryotic Cytochrome Oxidase I (COI)         |
+| phytoref     | +     | -      | -       | -      | eukaryotic plastid 16S rRNA                   |
+| zehr-nifh    | +     | -      | -       | -      | Nitrogenase iron protein NifH                 |
 | standard     | -     | -      | +       | -      | any in genomes of archaea, bacteria, viruses³ |
 
 ¹[`--dada_taxonomy_rc`](https://nf-co.re/ampliseq/parameters#dada_taxonomy_rc) is recommended; ²: de-replicated at 85%, only for testing purposes; ³: quality of results might vary
@@ -242,7 +244,7 @@ Special features of taxonomic classification tools:
 - QIIME2's reference taxonomy databases will have regions matching the amplicon extracted with primer sequences.
 - DADA2, Kraken2, and QIIME2 have specific parameters to accept custom databases (but theoretically possible with all classifiers)
 
-Parameter guidance is given in [nf-core/ampliseq website parameter documentation](https://nf-co.re/ampliseq/parameters/#taxonomic-database).
+Parameter guidance is given in [nf-core/ampliseq website parameter documentation](https://nf-co.re/ampliseq/parameters/#taxonomic-database). Citations are listed in [`CITATIONS.md`](CITATIONS.md).
 
 ### Metadata