16S_rRNA_bacterial_communities_analysis
The set of scripts for programming language R for analyzing genetic and taxonomic diversity of bacterial communities received by metagenomic data of 16S rRNA
The repository contains four zip files with scripts and primary data for data processing.
- Estimation of confidence intervals using the bootstrap method for the indexes of the diversity of the communities of Schennon and Simpson. Statistical analysis of the Schennon and Simpson indices.
Shenon_Simpson.zip
Contains files:
23.shared - table of the representativeness of the OTU of the species rank in the sample when analyzing the V2-V3 regions 16S rRNA
34.shared - table of the representativeness of the OTU of the species rank in the sample when analyzing the V3-V4 regions 16S rRNA
R_index.txt - script for data analysis
- Assessing species richness in samples using indexes Chao1 and ACE
Chao1_ACE.zip
Contains files:
23.shared - table of the representativeness of the OTU of the species rank in the sample when analyzing the V2-V3 regions 16S rRNA
34.shared - table of the representativeness of the OTU of the species rank in the sample when analyzing the V3-V4 regions 16S rRNA
R_script_chao.txt - script for data analysis
- Comparison of species diversity of communities at different levels of taxonomic organization (phylum, class, order, family) with the help of Bray-Curtis distance metric, Gower distance metric and Jaccard distance metric.
Taxon_diversity.zip
Contains files:
23.shared - table of the representativeness of the OTU of the species rank in the sample when analyzing the V2-V3 regions 16S rRNA
34.shared - table of the representativeness of the OTU of the species rank in the sample when analyzing the V3-V4 regions 16S rRNA
23.taxonomy - taxonomic identification of species level OTU for samples analyzed using the V2-V3 regions 16S rRNA
34.taxonomy - taxonomic identification of species level OTU for samples analyzed using the V3-V4 regions 16S rRNA
R_taxon.txt - script for data analysis
- Comparison of the genetic diversity of the communities at the level of representative sequences for the OTU species of rank
Genetic_diversity.zip
Contains files:
23.fasta - representative sequences for the OTU species of rank for samples analyzed using the V2-V3 regions 16S rRNA
24.fasta - representative sequences for the OTU species of rank for samples analyzed using the V3-V4 regions 16S rRNA
23_34.fasta - the closest full-length 16S rRNA sequences for each representative sequence from both regions that founded in the SILVA 123 database
R_seq_analiz.txt - script for data analysis