Petri: Flomics’ new 16S amplicon sequencing analysis pipeline on Stratus

Jul 24, 2023

By:

Cristina Tuñi, MSc

Bioinformatics Scientist

Julien Lagarde, PhD

Head of Bioinformatics

16S amplicon sequencing and metagenomics analysis have revolutionized the study of microbial communities 1. The availability of high-throughput sequencing technologies and new analysis algorithms has made it possible to analyze bacterial diversity in various environments. Petri, the new 16S amplicon sequencing analysis pipeline available on Stratus, enables in-depth analysis of bacterial diversity in various environments. Let’s explore how this advanced pipeline can empower your research.

Input data

The user can select from a comprehensive list of broadly used primer kits for Illumina and PacBio technologies. Petri supports a wide range of primer kits for Illumina and PacBio technologies, allowing you to tailor the analysis to your specific needs. Both single-end and paired-end samples are supported, with analysis parameters already set to the standard methods of analysis.

💡If you have several samples to analyze as part of the same study, we recommend uploading them in the same batch, to take full advantage of Petri’s powerful sample comparison features (example).

Seamless Sequence Quality Control

Petri’s first step is an automated sequence quality control process. By eliminating base-calling inaccuracies and adapter contamination, Petri ensures reliable downstream analysis. This comprehensive process includes trimming low-quality bases, removing adapter sequences, and filtering out overly short reads.

Accurate Sequence Alignment and Clustering

Once your sequencing data is quality-controlled, Petri performs precise sequence alignment and clustering. Aligning high-quality reads to up-to-date reference widely used databases, such as Greengenes2 and SILVA3, Petri identifies the closest known relatives of your sequences. Utilizing advanced clustering algorithms, similar sequences are grouped into Operational Taxonomic Units (OTUs)4 based on a defined sequence similarity threshold. This step lays the foundation for accurate taxonomic assignment.

Robust Taxonomic Classification

With Petri, taxonomic classification becomes a robust and efficient process. Leveraging well-established algorithms like DADA25 and QIIME26 that employ machine-learning techniques to assign taxonomic labels to each OTU. These algorithms have been extensively benchmarked7, demonstrating their reliability and accuracy. From phylum to species, Petri provides comprehensive taxonomic identities for your microbial communities.

Unveiling Microbial Diversity

Petri’s powerful pipeline enables you to explore microbial diversity in a simple manner. Calculating alpha diversity metrics (e.g., richness and evenness) within each sample and beta diversity metrics (e.g., UniFrac and Bray-Curtis distances) to compare diversity between samples, Petri reveals the intricate structure and composition of microbial communities in different environments. By grouping samples into different categories, you can easily uncover valuable insights about group diversity variations.

Interactive Reports and Visualizations

Petri goes beyond raw data by providing interactive reports and visually appealing visualizations. Dive into diversity bar plots, abundance heatmaps, and Principal Coordinates Analysis (PCoA) plots to uncover meaningful patterns and associations within your microbial samples. These intuitive visual representations help you interpret and present your results with clarity and impact. We also provide all pipeline results as a downloadable ZIP archive.

Heatmap comparing the abundance of OTUs between samples of the same analysis

Overview of species frequencies between samples of the same analysis

Effortless Analysis with Stratus

Experience the simplicity of Petri’s analysis pipeline through Stratustm, our automated cloud analysis platform. With just three clicks, select your primer kit, choose the reference database, and upload your samples. Petri takes care of the rest, automatically computing all the necessary steps in the background. Once the analysis is complete, you’ll receive an email notification, signaling that your results are ready for exploration and download.

Unlock the full potential of your 16S amplicon sequencing data with Petri on Stratus. Explore the fascinating world of microbial communities and drive your research forward with confidence and ease. Get started today and embark on a new era of scientific discovery!

Behind the Scenes

Petri is the work of Flomics bioinformaticians Cristina Tuñí and Julien Lagarde. We are grateful to the developers of the nf-core/ampliseq pipeline, on which Petri is built.

1. Johnson, J. S. et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat. Commun. 10, 5029 (2019).

2. DeSantis, T. Z. et al. Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB. Appl. Environ. Microbiol. 72, 5069–5072 (2006).

3. Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007).

4. Blaxter, M. et al. Defining operational taxonomic units using DNA barcode data. Philos. Trans. R. Soc. B Biol. Sci. 360, 1935–1943 (2005).

5. Callahan, B. J. et al. DADA2: High resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).

6. Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).

7. Straub, D. et al. Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline. Front. Microbiol. 11, (2020).