Metagenomics Analysis

This is a repository to reconstruct the analysis done for a metagenomics project. Only the rules to do the analysis are stored, since the actual data is too big to store online. One can however see which files have been changed by having a look at how the *_track.txt files have changed over the various commits.

Install Snakemake

Snakemake has been used to make the analysis reproducible. Snakemake uses python3. A common approach for handling Python scripts is to create a virtual environment for each of them so your modules of different python scripts do not interfer with each other. Here we use conda to install snakemake:

conda create -n py3-snakemake python=3 anaconda
source activate py3-snakemake
pip install snakemake

You can deactivate the environment again with:

source deactivate

Clustering metagenomic assemblies with CONCOCT

The idea is to cluster metagenomic assemblies of six related samples that we have into bins using CONCOCT. For this we follow the complete example.

Cutting up contigs

The assemblies have already been done, so they have been put in the config.json file. All the rules to do the analysis are in the Snakefile. Start by cutting up the contigs into chunks of 10K:

snakemake --cores 6 -p all_cutup_10K

This results in:

$ ls concoct/*/cutup/contigs_10K.fasta
concoct/101B/cutup/contigs_10K.fasta  concoct/103/cutup/contigs_10K.fasta  concoct/105/cutup/contigs_10K.fasta
concoct/102/cutup/contigs_10K.fasta   concoct/104/cutup/contigs_10K.fasta  concoct/106/cutup/contigs_10K.fasta