Overview

Bioinformatics became an integral part in our work in which we attempted to relate soil diversity to POP degradation. This section contains scripts and pipelines used across projects and was provided for transparancy and quality assurance.

Pre-processing of fastq sequences with Qiime2

Scripts used for pre-processing fastq files

From Qiime2 into R - Initial diagnostics

Importing .qza files into R, creating a phyloseq object and do some quality filtering

Diversity analysis

Some visualisations of alpha and beta diversity

Phylofactor differential abundance analysis

Differential abundance analysis using the package phylofactor

From ASVs to metabolic pathways with PICRUSt2

Predicting metabolic pathways from abundances of amplicon sequence variants (ASVs)