We have developed an integrated pipeline that combines all the steps required for analysis of 16S rRNA gene amplicon sequence data, using open source software. The pipeline is available through Github. Briefly, the pipeline accepts raw Illumina 16S rRNA reads (.fastq format), performs quality control (FastQC, MultQC), read filtering, read merging and OTU picking (usearch), taxonomic annotation (QIIME) and generates a phylogenetic tree of the OTUs. The resulting OTU table (.biom format) and phylogenetic tree (.tre format) can be imported into R for further analysis (please consult our Tools & Resources section for a tutorial on downstream processing of 16S data in R). The package is wrapped into a Nextflow pipeline (Nextflow is a workflow language that enables scalable and reproducible scientific workflows using software containers), which is accompanied by a configuration file whereby read processing parameters and a classification database can be predefined. The whole workflow is packaged in Singularity containers and this makes it portable to any system that has Singularity setup.