hands-on_1_setup.md

Hands-on session Day 4: Incidence estimation

Introduction

In this hands-on session we will be working with a pipeline tool called GInPipe implemented in Snakemake. This pipeline infers the trajectory of an effective population size (or incidence) for a viral pandemic from a collection of time-stamped viral sequences. The pipeline has so far been tested for SARS-CoV-2.

In brief: Viral sequence data is placed into redundant temporal bins. For each bin, a parameter is inferred that correlates with the effective population size estimate (or incidence) of the infection. GInPipe then smoothes over all derived parameters and reconstructs continuous trajectory of the effective population size estimate (or incidence) [1].

The pipeline uses the following dependencies:

- python=3.9.18
- snakemake=7.32.3
- biopython=1.78
- pandas=2.0.3
- scipy=1.11.1
- bbmap=38.18
- numpy=1.24.4
- matplotlib=3.7.2
- scikit-fda=0.8.1
- pysam=0.21.0
- seqkit=2.4.0
- samtools=1.17
- minimap2=2.26

Installation

1. Clone repository

git clone https://github.com/KleistLab/GInPipe

Or download the latest release: https://github.com/KleistLab/GInPipe/releases/tag/v3.0.0

2. Install (mini)conda

Conda will manage the dependencies of our pipeline. Installation instructions can be found here: https://docs.conda.io/projects/conda/en/latest/user-guide/install.

3. Create working environment

Switch to whatever directory you put the GInPipe repository into:

cd path/to/ginpipe

3.1. Create and activate environment

conda env create -f env/env.yml
# OR use, like before, a specific path to store the environment
conda env create -p envs/GInPipe3 -f env/env.yml

conda activate GInPipe3

3.2. If an error occurs, try to install packages via mamba

Follow the instructions to install Mamba: https://mamba.readthedocs.io/en/latest/mamba-installation.html

You should already have Mamba! If so, skip installation

Add channels where mamba/conda will look for the packages:

conda config --add channels r 
conda config --add channels agbiome
conda config --add channels conda-forge
conda config --add channels bioconda 
conda config --add channels anaconda   

Make an environment using mamba. Give it a different name to not cause conflicts with provided environment in env/env.yml, e.g. tutorial:

mamba create -y -p envs/tutorial bbmap pip seqkit samtools numpy pysam biopython pandas scipy minimap2 pyvcf

Activate the new environment:

conda activate envs/tutorial

4. Installation on M1/M2 Mac

If you have a newer Mac with M1/M2 chip some packages might not install via conda/mamba. If this is the case, follow instructions below.

Follow the instructions to install Mamba: https://mamba.readthedocs.io/en/latest/mamba-installation.html

Add channels where mamba/conda will look for the packages:

conda config --add channels r 
conda config --add channels agbiome
conda config --add channels conda-forge
conda config --add channels bioconda 
conda config --add channels anaconda   

Make a new environment using mamba skipping packages that mamba couldn't install (in this case pysam,samtools, seqkit and minimap2). Give it a different name to not cause conflicts with provided environment in env/env.yml, e.g. tutorial:

mamba create -y -p envs/tutorial bbmap pip numpy biopython matplotlib pandas scipy scikit-fda

Activate the new environment:

conda activate envs/tutorial

Install packages with pip:

pip install pysam

Install packages with brew (https://brew.sh)

brew install samtools
brew install seqkit
brew install minimap2

Next: initialize and run GInPipe

Reference

[1] Smith, M. R. and Trofimova, M., et al. (2021). Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020. Nature Communications 12, 6009. https://doi.org/10.1038/s41467-021-26267-y