Journal
SCIENTIFIC DATA
Volume 6, Issue -, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/sdata.2019.7
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Funding
- ISC SB RAS integration project 4.2. Application of the NGS-BD methods to ecological problems
- FASO [0345-2016-0007]
- Russian Foundation for Basic Research [18-34-00435_mol_a, 18-34-00442_mol_a]
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In this work, we compare the resolution of V2-V3 and V3-V4 16S rRNA regions for the purposes of estimating microbial community diversity using paired-end Illumina MiSeq reads, and show that the fragment, including V2 and V3 regions, has higher resolution for lower-rank taxa (genera and species). It allows for a more precise distance-based clustering of reads into species-level OTUs. Statistically convergent estimates of the diversity of major species (defined as those that together are covered by 95% of reads) can be achieved at the sample sizes of 10000 to 15000 reads. The relative error of the Shannon index estimate for this condition is lower than 4%.
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