| Summary: | Microbes in Tibetan permafrost This project repository associated with the following manuscript: Luyao Kang, Yutong Song, Rachel Mackelprang, Dianye Zhang, Shuqi Qin, Leiyi Chen, Linwei Wu, Yunfeng Peng and Yuanhe Yang*. Metagenomic insights into microbial structure and metabolism in alpine permafrost on the Tibetan Plateau. Structure <code>. ├── data1 ├── 16S ├── metadata.txt <--metadata including the climatic, vegetable for samples ├── otus.nwk <--phylogenetic tree for ASVs ├── otutab.txt <--ASV table ├── otutab_rare.txt <--Rarefy ASV table └── taxonomy.txt <--Taxonomic table ├── Functional genes ├── eggnog.KEGG_ko.raw.counts.txt <-- KEGG KO table with row counts └── eggnog.KEGG_ko.raw.tpm.txt <-- KEGG KO table with TPM tansformation ├── Metabolic ├── bin_abundance_table.tab <-- Abundance table for each bin ├── METABOLIC_result.xlsx <-- Summary of the presence/absence of functional genes on each genome ├── MW_score_result.csv <-- Resuts of metabolic weighted scores for the metagenomic assembly genomes └── tax.txt <-- Taxnomic identificcation for each bin └── Supplementary Data ├── Supplementary Data 1.xlsx <-- Characteristics of recovered metagenomic assembly genomes (MAGs) ├── Supplementary Data 2.xlsx <-- Custom selected KEGG genes used to define metabolic pathways └── Supplementary Data 3.xlsx <-- The metabolic profiles of all MAGs annotated by METABOLIC v4.0 └── script ├── read_data.R <-- codes for data input ├── amplicon_analysis.Rmd <-- microbial diversity and composition analysis based on the amplicon data ├── SPEC-OCCU.Rmd <-- specificity-occupancy analysis ├── env_effect_on_diver_comp.Rmd <-- test the environmentaL effects on the microbial community ├── iCAMP_analysis.R <-- null model analysis using iCAMP framework ├── selected_ko_analysis.Rmd <-- codes for the difference analysis in genes involved in C, N, S, and other elements among soil layers └── Metagenome_analysis.Rmd <-- codes for reproducing the results about the MAGs ...
|
|---|