CalmBelt

Rapid SARS‑CoV‑2 genome characterisation for outbreak tracking

CalmBelt's demo

Citation: Yingtaweesittikul, Hatairat, Karrie Ko, Nurdyana Abdul Rahman, Shireen Yan Ling Tan, Niranjan Nagarajan, and Chayaporn Suphavilai. "CalmBelt: rapid SARS-CoV-2 genome characterisation for outbreak tracking." Frontiers in Medicine: 2600.

Contact: suphavilaic@gis.a-star.edu.sg and hatairat.y@cmu.ac.th

How to run CalmBelt

1. Create conda environment

In this example, we use the lightweight miniconda.

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
conda create -n covid python=3.7

2. Installing required packages

A precompiled binary for iqtree2 can be downloaded from https://github.com/iqtree/iqtree2/releases/tag/v2.1.2. The remaining packages can be installed as follow:

conda activate covid 
conda install -c bioconda blast
conda install mafft 

git clone https://github.com/cov-lineages/pangolin.git 
conda env update -n covid --file pangolin/environment.yml 
cd pangolin 
pip install .
cd .. 

git clone https://github.com/neherlab/treetime.git
cd treetime
pip install .
cd ..

pip install -r requirement.txt 
conda install -c plotly python-kaleido

Toytree will require gs, so you might need to install ghostscript as well sudo apt-get install ghostscript.

3. Preprocessing your input genome set

This step would require users to prepare input files as follow:

• genome_dir contain fasta files
• genome_metadata.tsv contains region, clade, and lineage information
• world_metadata.tsv contains continent, clade, and lineage information of samples around the world (can be obtained from GISAID).

python preprecess.py genome_dir reference_fname reference_gene_loci predefined_clade predefined_label preprocess_dir world_metadata_fname country_name subsampling_n_samples

For example (an example dataset is available at calmbelt/preprocess.zip),

python preprocess.py genome_dir reference.fasta gene.tsv clade.tsv name_by_who.tsv preprocess world_metadata.tsv Singapore -1

4. Starting CalmBelt web application

python covid_app.py preprocess 

CalmBelt is based on Dash/Flask framework (default port = 8050), and users can access the website at http://localthost:8050. Additional information for deploying CalmBelt on a remote server is avilable upon request.