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updated README.md to mention phyloseq object creation
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a4000 committed Aug 8, 2023
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Expand Up @@ -40,6 +40,7 @@ By default, the pipeline currently performs the following:
- Taxonomical classification using DADA2, [SINTAX](https://doi.org/10.1101/074161) or [QIIME2](https://www.nature.com/articles/s41587-019-0209-9)
- Excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta diversity indices and plots thereof ([QIIME2](https://www.nature.com/articles/s41587-019-0209-9))
- Calls differentially abundant taxa ([ANCOM](https://www.ncbi.nlm.nih.gov/pubmed/26028277))
- Creates phyloseq R objects ([Phyloseq](https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html))
- Overall pipeline run summaries ([MultiQC](https://multiqc.info/))

## Usage
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