Amplicon-seq analysis

Ampliseq is a bioinformatics analysis pipeline used for 16S rRNA amplicon sequencing data.


Amplicon sequencing analysis workflow using DADA2 and QIIME2 -

When we run analysis

On request we may be able to run the nf-core “ampliseq” pipeline on your data (on a case-by-case basis). In order to run this pipeline we will require additional information from you. Please let NGI staff know if you would like us to run this pipeline for you and we will give you further information.

Input data

  • Fastq files
  • Primers used for amplification
  • Metadata for the samples
  • Reference database specific to the amplicon


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).

Last Updated: 15th May 2024

Please read our sample submission instructions before sending samples:

Sample Submission Guidelines
Method Status


We are currently testing this method. Please contact us to find out more.

Software tool versions

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Compatible Methods