How to Install Pilon 1.24 on Linux

Pilon is a bioinformatics software tool used for improving draft genome assemblies. It corrects bases, fixes misassemblies, and fills gaps by aligning sequencing reads to the draft genome. Pilon is particularly useful for refining assemblies from second-generation sequencing technologies like Illumina, making them more accurate and contiguous.

Prerequisites

Before installing Pilon, ensure that you have the following prerequisites:

1. Java Runtime Environment (JRE) version 11 or greater: Pilon requires Java to run.
2. SBT (Scala Build Tool): Needed to compile Pilon from source.

Step-by-Step Installation Guide

Step 1: Install Java

First, ensure you have Java installed. You can check if Java is installed by running:

java -version

If Java is not installed, you can install it using:

sudo apt update
sudo apt install openjdk-11-jdk

Step 2: Install SBT

Add the SBT repository and install SBT:

echo "deb <https://repo.scala-sbt.org/scalasbt/debian> all main" | sudo tee /etc/apt/sources.list.d/sbt.list
echo "deb <https://repo.scala-sbt.org/scalasbt/debian> /" | sudo tee /etc/apt/sources.list.d/sbt_old.list
curl -sL "<https://keyserver.ubuntu.com/pks/lookup?op=get&search=0xC99A6EFAE10A2942>" | sudo apt-key add
sudo apt-get update
sudo apt-get install sbt

If you encounter issues with the key server, you can manually download and install SBT as follows:

1. Download the SBT package:

    wget <https://github.com/sbt/sbt/releases/download/v1.5.5/sbt-1.5.5.tgz>
       
   

2. Extract the package:

    tar xzf sbt-1.5.5.tgz
       
   

3. Move the extracted files to a suitable location:

    sudo mv sbt /usr/local/sbt
       
   

4. Add SBT to your PATH:

    echo 'export PATH=/usr/local/sbt/bin:$PATH' >> ~/.bashrc
    source ~/.bashrc
       
   

Verify the SBT installation:

sbt sbtVersion

Step 3: Download Pilon

Download the Pilon 1.24 source code from the official repository:

wget <https://github.com/broadinstitute/pilon/releases/download/v1.24/pilon-1.24.jar> -P ~/Downloads

Extract the downloaded files:

cd ~/Downloads
mkdir pilon-1.24
mv pilon-1.24.jar pilon-1.24/

Step 4: Prepare the Build Environment

Create the necessary directory for the symbolic link:

mkdir -p ~/lib/pilon

Step 5: Build Pilon

Navigate to the Pilon directory and run the build script:

cd ~/Downloads/pilon-1.24
./build.sh

This script will compile Pilon using SBT, fetch all necessary dependencies, and create a symbolic link to the compiled jar file in ~/lib/pilon/pilon-dev.jar.

Step 6: Verify the Installation

Run the following command to verify that Pilon is installed correctly:

java -jar ~/lib/pilon/pilon-dev.jar --help

This should display the help message for Pilon, indicating that it is ready for use.

Using Pilon

To use Pilon for your genome assembly improvement tasks, you can run the following command, replacing genome.fasta, frags.bam, jumps.bam, and unpaired.bam with your actual file paths:

java -jar ~/lib/pilon/pilon-dev.jar --genome genome.fasta --frags frags.bam --jumps jumps.bam --unpaired unpaired.bam --output pilon_output

By following these steps, you should be able to successfully install and use Pilon 1.24 on your Linux system. If you encounter any issues, refer to the official Pilon documentation for additional guidance.