Amplicon-seq analysis
Ampliseq is a bioinformatics analysis pipeline used for 16S rRNA amplicon sequencing data.
nf-core/ampliseq
https:
Amplicon sequencing analysis workflow using DADA2 and QIIME2 - https://nf-co.re/ampliseq
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
Results
By default, the pipeline currently performs the following:
- Sequencing quality control (FastQC)
- Trimming of reads (Cutadapt)
- Infer Amplicon Sequence Variants (ASVs) (DADA2)
- (Optional) post-clustering with VSEARCH
- Predict whether ASVs are ribosomal RNA sequences (Barrnap)
- Phylogenetic placement (EPA-NG)
- Taxonomical classification using DADA2; alternatives are SINTAX, Kraken2, and QIIME2
- 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)
- Creates phyloseq R objects (Phyloseq)
- Pipeline QC summaries (MultiQC)
- Pipeline summary report (R Markdown)
Be aware that some functions are only available if Metadata has been provided.
Last Updated: 27th March 2026