This repository contains the code and resources used for analyzing the impact of sampling design on soil animal, bacterial, and fungal diversity estimates based on PacBio and Illumina amplicon sequencing. This repository eexplores the influences of sampling designs including sampling depth, sampling area, and sample size on the biodiversity estimation using individual samples, DNA and soil pooling samples.
get the tables.R: Script to rarefy the tables.get the sample size for 8 subsamples.R: Script to select 8 samples from GSMc62 (N62D0-5) sampling design and estimate the diversity for each combination.get the richness at different sequencing depths.R: Script to estimate diversity at various sequencing depths.similarity.comparison.R: Script to estimate the difference in community dissimilarity across pooling strategies.visualization and significant test.R: Generates figures used in the manuscript (e.g., accumulation curve).diversity comparison across sampling designs: including constrast of marginal effects in diversity across sampling designs; diversity comparison across sampling designs/effective number of designs.R: Script to estimate effective number of OTUs for each unpooled sampling design at summary sequencing depth.pooling effect on diversity across sampling designs: including the script to estimate the pooling effect and the effect of the sequencing depths on the diversity estimate.rare OTUs and artefacts: including the script to estimate the influence of sampling designs on the rare OTUs, rare OTUs, and artefacts.
https://mycology-microbiology-center.github.io/Soil_biodiversity_assessments/
Chen, M., Dulya, O., Mikryukov, V., Copot, O., Metsoja, M., & Tedersoo, L. (under review). Sampling design and sample processing affect soil biodiversity assessments.