Amplicon sequencing analysis workflow using DADA2 and QIIME2
*nfcore/ampliseq* is a bioinformatics analysis pipeline used for 16S rRNA amplicon sequencing data (currently supported is Illumina paired end data).
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.
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>
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
singularityand set the appropriate execution settings for your local compute environment.
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"
See usage docs for all of the available options when running the pipeline.
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.
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).
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
If you use
nf-core/ampliseq for your analysis, please cite the
ampliseq article as follows:
Daniel Straub, Nia Blackwell, Adrian Langarica-Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst *Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline* *Frontiers in Microbiology* 2020, 11:2652 doi: 10.3389/fmicb.2020.550420.
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:
*The nf-core framework for community-curated bioinformatics pipelines.*
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.