Metagenomics workshop

Applied meta-omics summer school

Day 3

Description

This repository has teaching materials for a hands-on metagenomics workshop going from metagenomic assemblies to metagenome-assembled genomes (MAGs) to biosynthetic gene clusters (BGCs) and more. This workshop is taught by Lucas Paoli (ETHZ) and Serina Robinson (Eawag).

Day 3 Schedule

Time	Topic	Instructor
08:30 - 09:00	Module 0: setting up the computational environment	Lucas & Serina
09:00 - 10:45	Module 1: assembly to bins	Lucas & Serina
10:45 - 11:00	15-min break	All
11:00 - 11:45	Seminar: Computational Tools for Genome Mining and Antibiotic Discovery	Nadine Ziemert
11:45 - 12:45	Lunch	All
12:45 - 13:45	Seminars by participants	All
13:45 - 14:00	15-min break	All
14:00 - 15:45	Module 2: bins to genomes	Lucas & Serina
15:45 - 16:00	15-min break	All
16:00 - 16:30	Seminar: Metagenome mining to tap microbial functional potential	Serina
16:30 - 17:30*	Module 3: choose your own (natural product) adventure	Serina & Lucas

*Flexible time to continue afterwards or on Friday in the Open Workshop Session

Before arriving at the workshop

0. Familiarize yourself with unix (here and/or here) and conda.

1. If you do not already have an ssh client as part of the operating system (e.g., if you have a Windows machine), download a third party software such as one of the following:

• MobaXterm
  
• PuTTY
  
• Cygwin
  

2. For file transfer on Windows, we recommend downloading winscp

Getting started at the workshop

3. Open your ssh client and connect to Cousteau (the ETH teaching server)

Click for instructions:

ssh [email protected]

• type your password
  
• press ENTER
  

If you already installed conda:

rm -r miniconda3

Then:

cp ../paolil/.bash_profile .
cp ../paolil/.bashrc .

4. Setting up conda

Click for instructions:

In your terminal type:

• wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

• bash Miniconda3-latest-Linux-x86_64.sh

• press ENTER, scroll down, type in ‘yes’
  

• press ENTER
  

• type in yes
  

• close and reopen session (exit then ssh cousteau)
  

• rm Miniconda3-latest-Linux-x86_64.sh
  

• Install should take ~5min
  

• Log out and log in again
• Add conda channels

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

• Install mamba (faster, alternative client to conda)

conda install mamba
mamba install git

• Set up default path for the conda environments (otherwise they will be installed in our home and we will run out of space)

mkdir -p /nfs/teaching/scratch/$USER/environments/
conda config --add envs_dirs /nfs/teaching/scratch/$USER/environments/

5. Preparing the conda environments for the workshop

Click for instructions:

• Set up three distinct conda environments for the three modules of the workshop as follows:

Module 1:

conda create -yn module-1
conda activate module-1
conda install -y metabat2
conda install -y samtools
conda install -y bwa
conda deactivate 

Module 2:

conda create -yn module-2
conda activate module-2
mamba install -y gtdbtk=2.3.0 checkm-genome=1.2.2
# ignore the commands to download the database and instead use the following:
export GTDBTK_DATA_PATH=/nfs/teaching/databases/gtdb/
echo "export GTDBTK_DATA_PATH=/nfs/teaching/databases/gtdb/" >> .bashrc
# Now let's finish setting up CheckM, please run the following to set up the database:
export CHECKM_DATA_PATH=/nfs/teaching/databases/checkm
echo "export CHECKM_DATA_PATH=/nfs/teaching/databases/checkm" >> .bashrc
conda deactivate

Module 3:

conda create -yn module-3
# we don't need to install anything there yet

6. Git clone the applied-meta-omics-ethz-2023/metagenomics-workshop Github repo

git clone https://github.com/applied-meta-omics-ethz-2023/metagenomics-workshop.git

7. If you're completed all the steps above, you are ready to go. We will get started with Module 1!