Introduction
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.
Quick Start
-
Install
nextflow
-
Install any of
Docker
,Singularity
orPodman
for full pipeline reproducibility (please only useConda
as a last resort; see docs) -
Download the pipeline and test it on a minimal dataset with a single command:
nextflow run nf-core/ampliseq -profile test,
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
in your command. This will enable eitherdocker
orsingularity
and set the appropriate execution settings for your local compute environment. -
Start running your own analysis!
nextflow run nf-core/ampliseq -profile --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.
Documentation
The nf-core/ampliseq pipeline comes with documentation about the pipeline: usage and output.
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.
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).
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).
Citation
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.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x. ReadCube: Full Access Link
Version History
2.11.0 (latest) Created 6th Aug 2024 at 04:03 by WorkflowHub Bot
Updated to 2.11.0
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1.0.0 (earliest) Created 11th Jun 2024 at 13:54 by WorkflowHub Bot
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Submitter
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Created: 4th Jun 2024 at 11:32
Last updated: 11th Jun 2024 at 13:54
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