mountainman12/sars-cov2-phylo

Analysis of the viral genomes of SARS-CoV2 using MAFFT and igtree

Phylogenetic analysis of SARS-COV-2 genomes using MAFFT and iqtree

Preparation before running the pipeline

We need to check for avaliablility of important software packages before we run the analysis

• Java: Open command line environment and type
  

java --version

If version is displayed, then your system contains java. Keep in mind that the software packages would run best using the javac 11.0.8

openjdk 11.0.8 2020-07-14
OpenJDK Runtime Environment (build 11.0.8+10-post-Ubuntu-0ubuntu120.04)
OpenJDK 64-Bit Server VM (build 11.0.8+10-post-Ubuntu-0ubuntu120.04, mixed mode, sharing)

If java is not found, install using command line

sudo apt-get update
sudo apt-get install default-jre

• curl: To check whether curl is installed

curl --version

If version information is not displayed, install curl using

sudo apt-get install curl

• Miniconda3: A bootstrap version of Anaconda for python packages, to check if conda is installed

conda -V

If version information is not displayed, then install (for a 64-bit system)

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh

Follow on-screen instructions until the installation is complete

NOTE: When asked to add conda_init , enter YES

Add conda to PATH

source ~/.bashrc

If the installation is successful, you should see a list of installed packages with

conda list

If the command cannot be found, add conda to PATH environment manually, open the bashrc file and add the export PATH command to the end of the file and save it.

sudo nano ~/.bashrc

export PATH=~/miniconda3/bin:$PATH

• BioPython: Package for running bioinformatics data analysis

To check if biopython is installed, run

pip list | grep biopython

If version is not returned, install using,

pip install biopython

Instructions for running the pipeline

STEP 1: Installation of software packages using conda

We will be installing the following software packages in our environment to run the pipeline. Version info. is also displayed which was used to run this pipelime

• MAFFT v7.471 (2020/Jul/3)
• iqtree (multicore version 2.0.3 for Linux 64-bit built Apr 26 2020)
• jalview (2.11.1.0)
• figtree (v1.4.4)

We will add the specific channels to our conda environment before installation, and install packages using a single bash script

bash packages.sh

STEP 2: Running the final pipeline

Once all packages are installed the pipeline can be executed using the bash script

bash pipeline.sh

The code working has been described in the documented version of the project

Acknowledgements

• Winfred Gatua (Kenya)
• Pawan Verma (India)
• Harinath. S (India)
• Ahmed El-Gammal (Egypt)
• Caroline Vilas Boas De Melo (Brazil)
• Maruf Ahmed Bhuiyan (Bangladesh)
• Oluwasefunmi Shodunke (Nigeria)
• Peter Josiah Aminu (Nigeria)
• Tracy-Allen Ezechukwu (Nigeria)

Contact:

Pawan Verma
Email: [email protected]
Twitter: @VP_312

sars-cov2-phylo's Issues

ERROR: Cannot read file seqalign.fasta

Hi there!

I am trying phylodynamics of SARSCoV2 using your pipeline. I am having the GISAID data for CoV2 and one Reference genome with which I want to do alignment using MAFFT and want to generate a phylogenetic tree, But I am getting following error: Reading alignment file seqalign.fasta ... ERROR: Cannot read file seqalign.fasta
opening the tree file
javax.swing.UIManager$LookAndFeelInfo[Metal javax.swing.plaf.metal.MetalLookAndFeel]
javax.swing.UIManager$LookAndFeelInfo[Nimbus javax.swing.plaf.nimbus.NimbusLookAndFeel]
javax.swing.UIManager$LookAndFeelInfo[CDE/Motif com.sun.java.swing.plaf.motif.MotifLookAndFeel]
javax.swing.UIManager$LookAndFeelInfo[GTK+ com.sun.java.swing.plaf.gtk.GTKLookAndFeel]
Exception while loading the ApplicationAdapter:
java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at jam.mac.Utils.registerDesktopApplication(Unknown Source)
at jam.framework.MultiDocApplication.initialize(Unknown Source)
at figtree.application.FigTreeApplication.main(Unknown Source)
Caused by: java.lang.UnsupportedOperationException: The APP_ABOUT action is not supported on the current platform!
at java.desktop/java.awt.Desktop.checkActionSupport(Desktop.java:380)
at java.desktop/java.awt.Desktop.setAboutHandler(Desktop.java:696)
at jam.java9only.ApplicationAdapter.registerApplication(Unknown Source)
... 7 more
I am not sure how to put the reference genome and genome files from GISAID in your code. Please help me to solve this issue