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Workshop: SARS-CoV-2 mutation profile

Mutation profiling with covsonar

We will use covsonar to create a database of mutation profiles and do some queries.

Check the covsonar GitHub README and install the tool in a conda/mamba environment.

# download the repository to the current working directory using git 
git clone https://github.com/rki-mf1/covsonar.git
# build the custom software environment using conda or mamba [recommended]
# ATTENTION: check where you are located and where you install the environment
mamba env create -p envs/sonar -f covsonar/sonar.env.yml
# activate the conda evironment if built 
conda activate envs/sonar

Let's get some example SARS-CoV-2 genomes:

# get example data, a collection of different SARS-CoV-2 lineages, full genomes
wget --no-check-certificate https://osf.io/wpk75/download -O sc2-genomes-diff-lineages.tar.gz
# extract the archive
tar zxvf sc2-genomes-diff-lineages.tar.gz
# create a multi FASTA file
cat sc2-genomes-diff-lineages/*.fasta > sc2-genomes-diff-lineages.fasta

Create a new covsonar DB:

# adding all sequences from 'sc2-genomes-diff-lineages.fasta' to database 'mydb'
# using four cpus (the database file will be created if it does not exist)
covsonar/sonar.py add -f sc2-genomes-diff-lineages.fasta --db mydb --cpus 4

Adding metadata information:

# get metadata TSV
wget --no-check-certificate https://osf.io/fwcv2/download -O sc2-genomes-diff-lineages.tsv

# importing lineage annotations and sampling dates from a custom TSV file to database 'mydb'
covsonar/sonar.py update --tsv sc2-genomes-diff-lineages.tsv --fields accession=acc date=sampling lineage=lineage --db mydb

Query genome sequences based on profiles and metadata information:

covsonar/sonar.py match --db mydb --include S:N501Y
covsonar/sonar.py match --db mydb --lineage B.1.1.7
covsonar/sonar.py match --db mydb --lineage B.1.1.7 --count
covsonar/sonar.py match --db mydb --lineage B.1.1.7 --include S:del:68:3 --count
covsonar/sonar.py match --db mydb --date 2022-01-01:2023-01-01 --count