5 Key features of Qiime 2 for your microbiome analysis

28 July 2021
Tianran Shi, Product Manager at Novogene AMEA

The microbiome field has undergone a shift from clustering-based methods of operational taxonomic unit (OTU) designation based on sequence similarity to denoising algorithms that identify exact amplicon sequence variants (ASVs). The Quantitative Insights Into Microbial Ecology (QIIME) microbiome bioinformatics platform has supported numerous microbiome studies. Its fidelity to the algorithms used and consistency in the analysis have gained a broad user and developer community. 

Novogene has recently updated its microbiome analysis pipeline using Qiime 2 from Qiime 1, offering customers ASVs analysis. Product manager Tianran Shi discusses the 5 key features of Qiime 2 that could help make your data analysis of amplicon sequences easier and make it possible to estimate the level of closely related species.

What is Qiime 2?

QIIME 2™(https://qiime2.org) is a new version of the microbiome analysis platform compare to Qiime 1. It was newly written in Python 3 and published online in the world's top academic journal Nature Biotechnology, on July 24, 2019.

It is a powerful tool for analyzing the microbiome community, allowing researchers to recapitulate the necessary steps in processing sequences from the raw data to the visualizations and interpretation of the results. Furthermore, it is open-source, and the analysis capability to enhance various aspects of microbiome analyses is crucial for the interpretation and credibility of results. 


5 Key Features of Qiime 2:

1. It makes annotation more accurate
Errors in Illumina-sequenced amplicon data are currently addressed by quality filtering and the construction of operational taxonomic units (OTUs). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. Each de-duplicated sequence generated after noise reduction using DADA2 is called ASVs (Amplicon Sequence Variants).
2. Results are traceable and repeatable with reproducibility
Qiime 2 automatically tracks your analyses with decentralized data provenance — no more guesswork on what commands were run! It iteratively records data provenance, ensuring bioinformatics reproducibility. Furthermore, you can also easily share results with your team, even those without QIIME 2 installed.

3. It provides many interactive visualization tools
It interactively explores your data with beautiful visualizations that provide new perspectives.

4. Plugin-based system — Your favorite microbiome methods all in one place
It has more than 20 kinds of plugins and is still developing to provide users with more than perfect services. One such plugin offered by Novogene is Picrust2 which provides function annotation for samples amplified at the 16S regions.

5. Different batches of data can be directly combined for analysis
Qiime 2 analyzes the exact sequence, merges analysis without re-clustering, and directly merges the feature sequence abundance table to carry out the follow-up standard analysis. Therefore, different batches of data can be directly combined for analysis.

Novogene has updated its microbiome analysis pipeline using Qiime2, offering customers ASVs analysis and species annotation, α- Diversity, β- Diversity. The pipeline of diversity, species diversity, and function prediction are as follows:

NovogeneAIT Genomics is a joint venture between Novogene and AIT Biotech, focusing primarily on the Asia Pacific, Middle East, and Africa (AMEA) region. We are a leading provider in genomic services and solutions for research and clinical applications, with operations in Singapore, Japan, Australia, India, Hong Kong S.A.R., China, the United States, the United Kingdom, and the Netherlands.


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