16S amplicon sequencing

This is how to perform 16S amplicon analyses.

Ampliseq pipeline

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

Quick start

• Latest stable release -r 1.1.0

A typical command would look like this

nextflow run nf-core/ampliseq -profile binac -r 1.1.0 \
--reads “data” \
--FW_primer "GTGYCAGCMGCCGCGGTAA" \
--RV_primer "GGACTACNVGGGTWTCTAAT" \
--metadata "metadata.tsv" \
--trunc_qmin 35 \
--classifier_removeHash

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

Known bugs

• 1.0.0 & 1.1.0 have a known bug that is why the --classifier_removeHash param should be used for these versions.

Reporting

There are no details about reporting yet.