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This project contains supplementary files used to produce the data presented in the paper entitled A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining.

Click here to download files. Other input files can be downloaded at NCBI website. Paired-end reads and contig files can be downloaded here.

We provide in folder cluster_analysis our source codes and additional files used to produce counting matrices of taxons and functions for clustering analysis listed below.

Folder inputs: contains one file that is used as input for Kaiju (kaiju_input.tar.gz) and two other files that were generated by Kaiju and Interpro tools and were used to generate counting matrices by the corresponding scripts.

Folder output: contains the expected counting matrices output for the scripts.

Folder scripts: contains five R scripts, described below:

• taxonomic_analysis.R: produces the taxonomic matrix
• taxonomic_cluster_plot.R: plots samples clustered by taxonomic composition
• taxonomic_stacked_plot.R: plots taxonomic composition of each sample
• functional_analysis.R: produces the functional matrix
• functional_cluster_plot.R: plots samples clustered by functions

Additionaly, we provide the following supplementary files in folder supplementary:

• quality: HTML files corresponding to quality reports of each read sample file obtained by FastQC tool (README.txt file contains a brief explanation about each report)
• SoilSamples.csv: a CSV file containing chemical metadata about each soil sample

If you have any trouble with these files, contact us by guilherme.oliveira@itv.org.