Introduction

nfcore/ampliseq is a bioinformatics analysis pipeline used for 16S rRNA amplicon sequencing data.

The workflow processes raw data from FastQ inputs (FastQC), trims primer sequences from the reads (Cutadapt), imports data into QIIME2, generates amplicon sequencing variants (ASV, DADA2), classifies features against the SILVA v132 database, 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, and finally calls differentially abundant taxa (ANCOM). See the output documentation for more details of the results.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

Documentation

The nf-core/ampliseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Pipeline configuration
   • Local installation
   • Adding your own system config
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

Credits

These scripts were originally written for use at the Quantitative Biology Center (QBiC) and Microbial Ecology, Center for Applied Geosciences, part of Eberhard Karls Universität Tübingen (Germany) by Daniel Straub (@d4straub) and Alexander Peltzer (@apeltzer).

Citation

If you use nf-core/ampliseq for your analysis, please cite it using the following DOI:

The pre-print can be cited as follows:

You can cite the nf-core pre-print as follows:

Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.