Trimming conditions for DADA2 analysis in QIIME2 platform

서지정보

ㆍ발행기관 : 대한구강생물학회 ㆍ수록지정보 : International Journal of Oral Biology / 46권 / 3호
ㆍ저자명 : Seo-Young Lee, Yeuni Yu, Jin Chung, Hee Sam Na

목차

Introduction
Materials and Methods
1. Sample data
2. QIIME analysis
Results
1. Sequencing quality score and assembled sequencescounts during pre-processing
2. Alpha diversity and taxonomic assignment
3. Trimming F270 in detail
Discussion
References

영어 초록

Accurate identification of microbes facilitates the prediction, prevention, and treatment of human diseases. To increase the accuracy of microbiome data analysis, a long region of the 16S rRNA is commonly sequenced via paired-end sequencing. In paired-end sequencing, a sufficient length of overlapping region is required for effective joining of the reads, and high-quality sequencing reads are needed at the overlapping region. Trimming sequences at the reads distal to a point where sequencing quality drops below a specific threshold enhance the joining process. In this study, we examined the effect of trimming conditions on the number of reads that remained after quality control and chimera removal in the Illumina paired-end reads of the V3–V4 hypervariable region. We also examined the alpha diversity and taxa assigned by each trimming condition. Optimum quality trimming increased the number of good reads and assigned more number of operational taxonomy units. The pre-analysis trimming step has a great influence on further microbiome analysis, and optimized trimming conditions should be applied for Divisive Amplicon Denoising Algorithm 2 analysis in QIIME2 platform.

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