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FarmMicrobiome

Description:

Metagenomic analyses of air microbiome and virome data from farms across degrees of urbanisation

This repository contains the scripts used for the analysis og the air metagenome data in the thesis titled: Characterisation of the air microbiome in farms with different degrees of urbanisation.

Content (folders):

  1. Shell_scripts: folder contains all the bash and python scripts used for the analysis of DNA sequences. Each file is named after the program used for the analysis (i.e., the file trimmomatic.sh contains the commands used for Trimmomatic).

  2. R_analysis: folder contains R and Rmarkdown files with the code used for statistical analysis of microbiome and virome data.

  3. Supplementary files: PDF with QUAST assessment of MEGAHIT assembly of all air samples.

  4. HTML files: notebook with python script for taxonomic annotation of viral contigs.