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Analysis of Microbiome data

Micriobial analysis aims to understand microbes and their functions in their environments. QIIME2 (Quantitative Insights Into Microbial Ecology) is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results.

We outline a pipeline to analyse 16S/18S paired-end sequencing data. Qiime2 can be used to analyse single-end and paired-end data.

Importing data into Qiime2

Data used and produced by qiime2 are stored as artifacts. Artifacts contain data and metadata and have a .qza extension. Qiime2 provides methods to view information (data and metadata) stored in artifacts by creating visualizations, that have a .qzv extension.

We import raw fastq files into qiime2. Depending on the sequencing platform used to generate the data, you will have data that has been de-multiplexed into sample specif fastq files, or not. The MiSeq platform at BecA-ILRI Hub will de-multiplex the data and we get sample specific fastq files.

Read more about different data types and importing them into qiime2 for anlaysis. We will be importing data described as type Cassava 1.8 paired-end de-multiplexed fastq.

To import fastq files;

#i create a directory to store all my artifact i.e '.qza' and the related visualization i.e '.qzv' files.

mkdir /home/mydir/qiime2_data/

#import the fastq files

qiime tools import \
 --type 'SampleData[PairedEndSequencesWithQuality]' \
 --input-path /home/mydir/qiime2_data/ \
 --input-format CasavaOneEightSingleLanePerSampleDirFmt \
 --output-path /home/mydir/qiime2_data/my_raw_data.qza

We mentioned that qiime2 provides method to summarize and view artifacts by storing them as visualizations, .qzv, files. The .qzv files can be opened on any browser using qiime viewer. To create visualization for the imported data;

qiime demux summarize \
 --i-data  /home/mydir/qiime2_data/my_raw_data.qza \
 --o-visualization /home/mydir/qiime2_data/my_raw_data.qzv

Qiime2 data filtering and feature (OTU) table construction

Qiime2 provides two pluggins/methods for filtering your sequences to the required quality and length.Sequence Variants are then selected from quality filtered data and the results are feature tables better known as OTU tables and the representative feature sequences. These methods are Dada2 and Deblur.

Important to keep in mind is the size of the amplified region covered by the primers used and what is the expected fragment length after read joining? This will determine the trim and truncate length parameters for dada2 and deblur pipelines.


The Dada2 pipeline detects and corrects illumina amplicon sequence data and additionally filter any phiX reads identified in sequencing data and also filter out any chimeric sequences. To see usage and parameters that can be adjusted get the help for the pluggin i.e

qiime dada2 --help

The data we are using is paired-end, hence we will use the qiime dada2 denoise-paired pluggin.

Key parameters in quality control of the sequences are those used to trim the forward, –p-trim-left-f; –p-trunc-len-f and reverse –p-trim-left-r; –p-trunc-len-r reads. The

population-diversity/microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data.1588166248.txt.gz · Last modified: 2020/04/29 13:17 by bngina