Scripts of Garrido-Oter et. al, Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia, in press.
originally by Ruben Garrido-Oter
These scripts are made available to facilitate reproducibility of our research. If you re-use any or part of this code, please reference with comments and cite our paper! Raw data and intermediate results necesary to run these scripts can be downloaded here.
Scripts used for processing data, creating the figures and performing the statistical analysis reported in the manuscript.
Configuration script containing paths to scripts and data as well as parameters for custom scripts and third-party tools.
Bash script containing ancilliary functions for whole-genome assembly.
Script used to assemble the genomes using SOAPdenovo and A5. It can be run in parallel using either the custom script bellow or the gnu parallel suit.
Custom script to run bash functions in parallel in a multi-core machine.
R script used to generate assembly statistics as well as GC and k-mer spectral projections. The output of this script contains clean assemblies (all contigs <1,000 bp are removed) as well as a PDF file containing a report which was used to manually inspect for likely contaminated assemblies.
datagen.functions.sh, compgen.functions.sh, and phylo.functions.sh
Bash scripts with ancilliary functions for gene calling and parsing of assemblies and ORF fasta files.
Bash script to perform parallel (opt. serial) processing of the whole-genome assemblies, including gene calling, quality filtering, parsing of the FASTA files, annotation, and phylogeny inference.
R script containing paths to data, intermediate results and output folders for the figures and statistical analyses.
plotting_functions.R and colors.R
R scripts containing functions and variables using for plotting (e.g. colors, ggplot2 themes, etc.)
R script to perform dimmensionality reduction of genome functional profiles and plotting.
Reference-based 16S rRNA amplicon profiling meta-analysis of Rhizobiales community structure and diversity:
Script to process 16S amplicon data from previous studies from raw data using a standarized pipeline. The output consists of joint OTU tables, FASTA files containing reference sequences, taxonomy classification, as well as multiple alpha- and beta-diversity estimates.
Auxiliary functions to perform meta-analysis of 16S data.
Configuration script containing paths to scripts and data as well as parameters for custom scripts and third-party tools.
Script to pre-process data from Schlaeppi et al., 2012 (Arabidopsis root and rhizosphere).
Script to pre-process data from Schlaeppi et al., 2014 (Arabidopsis and relatives root and rhizosphere.
Script to pre-process data from Schlaeppi et al., 2015 (Barley root and rhizosphere).
Script to pre-process data from Bai et al., 2015 (Arabidopsis root).
Script to pre-process data from Bai et al., 2014 (Arabidopsis leaf).
Script to pre-process data from Zgadzaj et al., 2016 (Lotus root, rhizosphere and nodules).
R script to perform CSS normalization of the joint OTU table.
Script to process data from joint analysis of 16S published studies.
Script to plot cumulative relative abundances of rhizobiales across hosts and micro-habitats.
Script to plot beta-diversity of rhizobiales communities across hosts and micro-habitats.
For any questions regarding these scripts, please contact
Ruben Garrido-Oter