This repository contains scripts (PBS and Python) and part of the data analysis for the UCL BIOC3301 project.
Read the project report here.
Scripts that were submitted to the Cirrus HPC via the portable batch system. Contains the basic QIIME pipeline (OTU assigning, filtering, and demultiplexing) as well as scripts used for further analysis (e.g. beta-diversity or construction of OTU table for specific taxonomy level). This foler does not contain scripts used on a local machine, however, the full list of available scripts can be found at http://qiime.org/scripts/index.html.
This foler stores tsv files that contain external data both for our project and the Earth Microbiome Project (EMP). They include physicochemical properties of the soil, location, temperature, etc. Note that the EMP dataset was filtered to contain only soil samples (i.e. the marine sediments, etc. were excluded).
ipynb scripts for analysis and manipulation of our and EMP data.
This folder contains data required to construct the phylogenetic tree (representative sequences were picked and aligned) and the tree file itself. The Phylo.io resouce is convenient for tree visualisation.
correlations contains txt files which are output of various correlation analyses applied to our project and EMP data.
figures stores images (graphs, phylogenetic tree), some of which were used in the report.
taxa_summary stores OTU tables for specific taxonomy levels (L1-L6) rarefied at a depth of 600 reads.