From cd7cedfdb994ca020c68a73dc28a30683b56bb19 Mon Sep 17 00:00:00 2001
From: Merit Kayastha <90002479+mkayasth@users.noreply.github.com>
Date: Wed, 1 May 2024 00:43:35 -0400
Subject: [PATCH] Update README.md
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- AdvBIIN-Project: ViralGeneClock.
-
Introduction
Using ViralGeneClock, the users can deposit the whole genome sequence (WGS) of different strains of a virus. The tool then examines the evolutionary relationship of the strains, and also estimates the relative mutation rates of the genes across these strains. It leverages Prokka for viral genome annotation, Muscle for multiple sequence alignment of each gene for different strains and the Neighbor Joining Algorithm for determining genetic distances and branch lengths. ViralGeneClock utilizes the genetic distance and branch length data to then provide relative mutation rates for each annotated gene. This is primarily a Linux tool developed through the Linux subsystem; the environment for running ViralGeneClock can be simulated using Github's Codespaces.
The final .zip folder is emailed to the provided address. Outputs from the full genome analysis is saved in the folder fullSequence-output. Results from gene-specific analyses are saved in the folder geneAnalysis-output, and the output for relative mutation rates is saved in the folder avg_mutation_rate_final.
+ Installations
+Create a new Github codespace, and clone the repository mkayasth/viralGeneClock--codespaces into your codespace. Using the terminal of the codespace, install the following dependencies:
+
+1) Prokka:
+Use the Bioconda channel to install Prokka:
+
+ ```shell
+conda install -c conda-forge -c bioconda -c defaults prokka
+```
+
+2) MUSCLE:
+
+ ```shell
+wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux32.tar.gz
+tar -zxvf muscle3.8.31_i86linux32.tar.gz
+chmod +x muscle3.8.31_i86linux32
+```
+
+3) Python3 Dependencies:
+
+```shell
+pip install matplotlib
+pip install biopython
+pip install flask
+pip install flask-mail
+```
+
+ Usage
+After completing necessary installations, run the web app with app.py :)
+
+ ```shell
+python3 app.py
+```
+
+Alternatively, you can use the command line interface with main.py (app.py calls main.py using the subprocess library).
+ ```shell
+python3 main.py
+```
+The comprises the complete set of whole genome sequences (WGS) for the strains you intend to analyze. Each strain's FASTA header should be the name of the strain.