ncov19_cytosine_depletion

Installation with conda

git clone https://github.com/HKU-BAL/ncov19_cytosine_depletion.git
cd ncov19_cytosine_depletion/
conda env create -f environment.yml
conda activate ncov19-ca
npm install

Nextstrain is also required, please follow the installation guide in the page.

Basic Usage

• Use crawler.ts to download fasta from GISAID.
• Run align_fasta.py, cleanup.py, count_byday.py, plot.py, update_intro.py and concat_fasta.py in order for processing the downloaded fasta.

Important notes

• All scripts modify files under the base_folder, which is defined and if needed, should be modified in both params.py and crawler.ts. Default is inside download_data/ under this directory.
• The repository of Nextstrain/ncov need to be referenced in params.py after the ncov_folder variable.
• base_folder/fasta/ stores the .fasta and .info retrieved directly from GISAID.
• base_folder/aligned_fasta/ stores the aligned fasta against the reference.
• base_folder/processed_fasta/ stores the raw sequence from fasta that is qualified (sequence length>29k, N<5%), while base_folder/backup_fasta/ stores those that is not.