Pipeline for the analysis of SARS-CoV-2 tiled amplicon sequencing data
git clone https://github.com/ngs-fzb/SARSCOV2seq
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
git clone https://github.com/cov-lineages/pangolin
cd pangolin
conda env create -f environment.yml
conda activate pangolin
pip install .
conda deactivate
conda create --name mtbseq
conda activate mtbseq
conda install -c bioconda mtbseq
conda deactivate
For more information on MTBseq click here: https://github.com/ngs-fzb/MTBseq_source
Copy reference .fasta and _genes.txt annotation from the SARSCOV2seq/Ref directory to the mtbseq /ref/ directory!
conda create --name ivar
conda activate ivar
conda install -c bioconda ivar
conda deactivate
Open the sarscov2seq file in a text editor and set paths to match the actual location of the "Ref" and "Scripts" directory on your computer. Default ARTIC amplicon set is v4.1.
Fastq files need to be in the format required by MTBseq please read the MANUAL.md.
Change to the directory containing your fastq files, copy sarscov2seq to the directory and change parameters as needed, afterwards execute:
sarscov2seq