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update README
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@d4straub
d4straub committed Jul 27, 2023
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Expand Up @@ -40,7 +40,8 @@ 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))
- Overall pipeline run summaries ([MultiQC](https://multiqc.info/))
- Pipeline QC summaries ([MultiQC](https://multiqc.info/))
- Overall pipeline html report ([R Markdown](https://github.com/rstudio/rmarkdown))

## Usage

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