NGS-SARS-CoV-2

This repository for NGS analysis of SARS-CoV-2 virus.

Aim

Project is aimed to perform NGS analyse of SARS-CoV-2 virus. This is my independent as well as preliminary work for biohackathon. Analysis would be cotain steps for upstream and downstream analysis of SARS-CoV-2 RNASEQ data. Result would be a case study of virus genome using available NGS analysis pipelines.GALAXY main toolshed contains hosted pipelines or workflows for the purpose. We will utilise available GALAXY reourses to analyse SARS-CoV-2 virus genome.

Background

This is the mean time of SARS-CoV-2 outbreak and COVID-19 endemic. Whole scientific community and common citizens are collective to get over the endemic. Citizen scince and virtual community is the felt need of the time. There have been significant progress into open science as developing open source software platforms and infrastrucure. Biohackathons are effective one to crowdsourse research studies and results. We can contribute to maximum and benefit humanity if all disciplines of research over SARS-CoV-2 virus come up together.

GALAXY is an eminent example of citizen science. It provides computational resources to biologists who are interested into NGS analysis.

Materials

SARS-CoV-2 RNASEQ data - GALAXY server - public GALAXY server or local GALAXY instance. Linux operating system. GALAXY workflows -

Methods

Study implements three GALAXY workflows for the case study of SARS-CoV-2 virus genome. These can be categorised as follows.

1. Denovo assembly and downstream analysis.
2. Reference based assembly and downstream analysis.

Downstream analysis steps include align and estimate abundance of gene expression, differential expression of genes and blast based annotation of obtained peptides.

Workflow setup.

Results

1. Denovo assembly and downstream analysis.
2. Reference based assembly and downstream analysis.

Discussions and Conclusions

Future work