Metagenomics 16S analysis

When using our 16S pipelines, all you would need are your raw reads and the sample metadata. Our pipelines will seamlessly process your data and give you the desired analysis results within no time. With just one click, the output files can be loaded in QIIME2 View, making it easy for you to interactively explore your results and make the breakthrough you've been waiting for.

16S microbiome analysis pipeline

16S rRNA sequencing is a NGS technique for identifying, classifying and quantifying microbes in different samples. It’s commonly used for getting a broad overview of the microbial community along with its phylogeny. These results can then be compared across different samples to identify statistical significance.

The pipeline uses modules provided by QIIME2 to orchestrate end-to-end microbiome analysis of the 16S sequencing data. The pipeline provides quality control and filtering, taxonomic classification, alpha and beta diversity, and differential abundance analysis, amongst other functionalities. All the steps in the pipeline are based on open source reference bioinformatics tools, considered as standards for 16S rRNA analysis.

  • dada2-denoise: Perform sequence quality controls

  • taxa-barplot: Visualize taxonomic composition

  • phylogeny-tree: Build phylogenetic trees

  • alpha-diversity: Calculate alpha-diversity

  • beta-diversity: Calculate beta-diversity

  • emperor-plot: Visualize sample ordination

  • composition-ancom: Test for microbiome composition differences


The pipeline provides multiple interactive plots and tables to explore the analyzed data.

  • Price: $50 - $70

    Average per analysis

  • Runtime: 6 hrs

    Average per analysis

Why BatchX

BatchX offers a serverless infrastructure for running bioinformatics analyses as a fully managed service. With the click of a button, off-load all your complex processing requirements to the cloud in a cost-effective, secure, and scalable way.

Take full control of your analysis

Our metagenomics pipeline gives you the flexibility to customize it to suit your needs. It's super easy to change any parameter and re-run the analysis with the click of a button.

Bioinformatics analysis made easy

Our no code environment gives you the freedom you need to run the metagenomics pipeline with zero coding required. Share your results with collaborators in a secure and private manner.

Custom support

Get instant assistance for any issue from our extended and experienced bioinformatics team through dedicated slack channels, emails, or conference calls.

Our users love us

BatchX allows us to carry out the metagenomic analyses we need quickly and efficiently. The platform’s flexibility and the availability of the team allowed us to improve and adapt the workflows to meet our needs. As a rookie in bionformatics, BatchX is a source of inspiration, showing me how far bioinformatic analyses can go.

Ignacio Montero

Bioinformatician, Microviable Therapeutics

BatchX is super easy to use. Any bioinformatician who deals with complex pipelines including 16S will appreciate the efficiency – import scripts once and never worry about recurring errors. We also enjoyed per job cost updates.

Adrian Santiago Ortiz

Bioinformatician, IMOMA

16S Metagenomics — one pipeline doesn’t fit all

TLDR: BatchX includes pipelines for classic 16S Metagenomics analysis but has also designed solutions for less conventional and more challenging scenarios. Read in this blog how BatchX can help you analyze 16S non-....