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The following script uses the “qiime tools import” to import the 172 FASTQ files onto a

single QIIME2 artifact “demux-yoga.qza” in the “inputs” directory:

qiime tools import \

--type ‘SampleData[PairedEndSequencesWithQuality]’ \

--input-format PairedEndFastqManifestPhred33 \

--input-path data/manifest.txt \

--output-path inputs/demux-yoga.qza

We will use this artifact “demux-yoga.qza” in the next step.

7.3.4  Raw Data Preprocessing

All the raw FASTQ files are contained in a single QIIME2 artifact. The next step would be

data preprocessing, which includes quality control and denoising.

7.3.4.1  Quality Assessment and Quality Control

QIIME2 has plugins for quality assessment and quality control. We can use “q2-demux

summarize” to assess the quality of the raw data in the artifact. The output of that com-

mand is a visualization file containing the quality assessment report that can be viewed

on an Internet browser. To keep the files organized, we can create a subdirectory to the

visualization file called it “viz”.

mkdir viz

Then, we can run the following script to save the report visualization file in the “viz”

subdirectory:

qiime demux summarize \

--i-data inputs/demux-yoga.qza \

--o-visualization viz/demux-yoga-qc.qzv

FIGURE 7.6  Manifest file for the example FASTQ files.