nf-core/ampliseq: a versatile, comprehensive, and reproducible amplicon sequencing analysis pipeline

I'd like to advertise nf-core/ampliseq (,, a bioinformatics analysis pipeline used for amplicon sequencing.

The pipeline is simple to install (requires nextflow and any container software, identical to all other nf-core pipelines), allows a variety of input data (Illumina, IronTorrent, PacBio using DADA2), supports many databases out of the box (e.g. SILVA, UNITE, PR2, GTDB), produces intuitive and interactive output (using QIIME2), and reports extensive quality control measures. nf-core/ampliseq runs on almost any compute infrastructure including laptops (Unix; Windows only with WSL2), compute clusters, or AWS cloud.

There is comprehensive documentation on how to run any nf-core pipeline (Getting started » nf-core) and install required components (Installation » nf-core). A video introduction to nf-core/ampliseq can be found at and documentation at, including usage, pipeline parameters, and example output.

In case there are any questions about the usage of the pipeline, open an issue in the github repo and/or join the nf-core community slack with general help (#help) or the ampliseq specific channel (#ampliseq).

The first release of the pipeline was in 2018 in the nf-core ( pipeline set and it was continuously maintained since then. The pipeline is a community effort (as is nf-core) and contributions and suggestions for improvements are welcome (and were frequent in the past).


Thanks @DaS ! FYI, I am recategorizing this topic as "Other Bioinformatics Tools", which is the appropriate category for external QIIME 2-compatible tools. The "Community Contributions" category is rather specific to QIIME 2-specific resources (e.g., plugins, tutorials).

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Thanks Nicholas, I was not exactly sure which category is appropriate! While I do browse occasionally topics in this interesting forum, I am not that familiar with its divisions.