nfcore/ampliseq repository overview

16S rRNA amplicon sequencing analysis workflow using QIIME2.

⁠Introduction

nfcore/ampliseq is a bioinformatics analysis pipeline used for 16S rRNA or ITS amplicon sequencing data (currently supported is Illumina paired end or PacBio).

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 containers making installation trivial and results highly reproducible.

⁠Quick Start

1. Install nextflow⁠

2. Install any of Docker⁠, Singularity⁠ or Podman⁠ for full pipeline reproducibility (please only use Conda⁠ as a last resort; see docs⁠)

3. Download the pipeline and test it on a minimal dataset with a single command:

   nextflow run nf-core/ampliseq -profile test,<docker/singularity/podman/conda/institute>
   

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   Please check nf-core/configs⁠ to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

4. Start running your own analysis!

   nextflow run nf-core/ampliseq -profile <docker/singularity/podman/conda/institute> --input "data" --FW_primer GTGYCAGCMGCCGCGGTAA --RV_primer GGACTACNVGGGTWTCTAAT --metadata "data/Metadata.tsv"
   

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See usage docs⁠ and parameter docs⁠ for all of the available options when running the pipeline.

⁠Pipeline Summary

By default, the pipeline currently performs the following:

• Sequencing quality control (FastQC⁠)
• Trimming of reads (Cutadapt⁠)
• Illumina read processing with QIIME2⁠
• Infer Amplicon Sequence Variants (ASVs) (DADA2⁠)
• Taxonomical classification based on SILVA⁠ v132⁠ or UNITE⁠ 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 (QIIME2⁠)
• Calls differentially abundant taxa (ANCOM⁠)
• Overall pipeline run summaries (MultiQC⁠)

⁠Documentation

The nf-core/ampliseq pipeline comes with documentation about the pipeline: usage⁠ and output⁠.

⁠Credits

nf-core/ampliseq was originally written by Daniel Straub (@d4straub⁠) and Alexander Peltzer (@apeltzer⁠) for use at the Quantitative Biology Center (QBiC)⁠ and Microbial Ecology, Center for Applied Geosciences⁠, part of Eberhard Karls Universität Tübingen (Germany).

We thank the following people for their extensive assistance in the development of this pipeline (in alphabetical order):

• Daniel Lundin⁠
• Diego Brambilla⁠
• Emelie Nilsson⁠
• Jeanette Tångrot⁠
• Sabrina Krakau⁠

⁠Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines⁠.

For further information or help, don't hesitate to get in touch on the Slack #ampliseq channel⁠ (you can join with this invite⁠).

⁠Citations

If you use nf-core/ampliseq for your analysis, please cite the ampliseq article as follows:

You can cite the nf-core/ampliseq zenodo record for a specific version using the following doi: 10.5281/zenodo.1493841⁠

You can cite the nf-core publication as follows: