Jia-Xiu/Jia_et_al_ISMECOMMS_2022

Unravelling the interplay of ecological processes structuring the bacterial rare biosphere

Unravelling the interplay of ecological processes shaping the bacterial rare biosphere

The following is the scripts related to the manuscript: Unravelling the interplay of ecological processes shaping the bacterial rare biosphere, authored by Xiu Jia, Francisco Dini-Andreote and Joana Falcão Salles. For recent updates, please go to https://github.com/Jia-Xiu/collaborations/tree/main/Araujo_et_al_2022.

Using QIIME2/2018.2 for cDNA sequences analysis

Work at QIIME2/2018.2 environment, using the following script

• script_cDNA_DADA2_20181026.txt

Using R for downstream analysis

Using R to integrate feature table with taxonomic infomation

• format_featuretable.R

alpha & beta-diversity analysis for the whole dataset

• alpha_beta_diversity.R

Sample-specific rarity cutoffs

• sample_specific_rarity_cutoffs.R

Analysis for the rare and common biospheres

• Rare_biosphere.R
• types_of_rarity_commonness.R

Taxa summarize

• Taxa_summarize.R

Community Assembly

• https://github.com/stegen/Stegen_etal_ISME_2013
• Fraction.Assembly.Processes_github.R

Authors

• Jia, Xiu
• Email: xibeihenai@gmail.com