16S amplicon sequencing

This is how to perform 16S amplicon analyses. A video explanation of the biology, the bioinformatics problem and the analysis pipeline can be found for version 2.1.0 in the nf-core bytesize talk 25.

Ampliseq pipeline

To perform 16S amplicon sequencing analyses we employ the nf-core/ampliseq pipeline.

Quick start

• Latest stable release -r 2.4.1

A typical command would look like this

nextflow run nf-core/ampliseq -profile cfc -r 2.4.1 \
--input “data” \
--FW_primer "GTGYCAGCMGCCGCGGTAA" \
--RV_primer "GGACTACNVGGGTWTCTAAT" \
--metadata "metadata.tsv" \
--trunc_qmin 35

Sequencing data can be analysed with the pipeline using a folder containing .fastq.gz files with direct fastq input or samplesheet input, also see here.

See here the info on how to create the metadata.tsv file.

If data are distributed on multiple sequencing runs, please use --multipleSequencingRuns and note the different requirements for metadata file and folder structure in the pipeline documentation

Reporting

There are no details about reporting yet. Please refer to the output documentation.