covid19S

A bioinformatic protocol for calling spike protein variants of SARS-CoV-2

To run with Docker

git clone https://github.com/jade-nhri/covid19S.git

cd covid19S

docker build -t "covid19s:v1" ./

docker run -h covidS --name covidS -i -t -v /:/MyData covid19s:v1 /bin/bash

Please note that you need to run “vdb-config --interactive” before using sra toolkit.

Installation

Installation from source

cd /opt

git clone https://github.com/jade-nhri/covid19S.git

cd covid19S/covid19S

chmod +x *.py

export PATH="$PATH:/opt/covid19S/covid19S"

Dependencies

• pyspoa-0.0.3
• medaka-1.2.6
• minimap2
• samtools
• bcftools
• seqkit=0.15
• sratoolkit

FASTQ files

BC20.fastq, Ct28

BC59.fastq, Ct31

https://drive.google.com/drive/folders/1cK9hx2wYnr-OvxfaW0rpS_wv-Dci0sJZ?usp=sharing

Usage

• readme