How to Run SSPACE Basic for Genome Assembly Scaffolding

SSPACE Basic is a powerful tool used in bioinformatics to improve the contiguity of genome assemblies by scaffolding contigs using paired-end and mate-pair sequencing data. This guide will walk you through the steps to correctly run SSPACE Basic on a Linux system, from installation to execution, using detailed code examples.

Prerequisites

Before starting, ensure you have:

• A Linux system
• Basic knowledge of the command line
• Internet connection for downloading the tool
• Installed Perl and necessary Perl modules

Step 1: Download and Install SSPACE Basic

1. Download SSPACE Basic:

    wget <http://bioinfo.genomics.org.cn/SSPACE/SSPACE_Basic_v2.0.tar.gz>
       
   

2. Extract the Tarball:

    tar -xvzf SSPACE_Basic_v2.0.tar.gz
       
   

3. Navigate to the SSPACE Directory:

    cd SSPACE_Basic_v2.0
       
   

4. Ensure Dependencies: Make sure Perl is installed and the necessary modules are available:

    perl -v
    sudo cpan Getopt::Long
    sudo cpan File::Basename
       
   

Step 2: Add SSPACE Basic to Your PATH

To run the SSPACE Basic script from anywhere, add its directory to your system’s PATH environment variable.

1. Open Your Shell Configuration File: For Bash:

    nano ~/.bashrc
       
   

   For Zsh:

    nano ~/.zshrc
       
   

2. Add the SSPACE Directory to PATH:

    export PATH=$PATH:/path/to/SSPACE_Basic_v2.0
       
   

3. Source the Configuration File: For Bash:

    source ~/.bashrc
       
   

   For Zsh:

    source ~/.zshrc
       
   

Step 3: Prepare Input Files

1. Scaffolds File: Ensure your scaffolds file is in FASTA format. Example:

    /path/to/your/balance_SC.fasta
       
   

2. Libraries File: Create a libraries.txt file containing information about your paired-end reads:

    lib1 /path/to/unmapped_SCOMGI1_1.fastq /path/to/unmapped_SCOMGI1_2.fastq 500 0.05 FR
       
   

Step 4: Running SSPACE Basic

Navigate to the directory containing your files and run the command:

cd /path/to/your/files/
perl /path/to/SSPACE_Basic_v2.0/SSPACE_Basic.pl -l libraries.txt -s balance_SC.fasta -x 1 -T 16 -b SCoutput_folder

Detailed Command Breakdown

• l libraries.txt: Specifies the file with library information.
• s balance_SC.fasta: Specifies the input scaffolds file.
• x 1: Indicates to extend the contigs.
• T 16: Specifies the number of threads to use.
• b SCoutput_folder: Base name for your output files, effectively specifying the output directory.

Example Directory Structure

Ensure your directory structure looks like this:

/path/to/your/files/
  ├── balance_SC.fasta
  ├── unmapped_SCOMGI1_1.fastq
  ├── unmapped_SCOMGI1_2.fastq
  └── libraries.txt

Example Libraries File

Here’s an example libraries.txt file with one library:

lib1 /path/to/unmapped_SCOMGI1_1.fastq /path/to/unmapped_SCOMGI1_2.fastq 500 0.05 FR

Troubleshooting

1. Invalid File Paths: Ensure all file paths are correct and accessible.

2. Permissions: Make sure files have the appropriate read permissions:

    chmod +r /path/to/your/files/*
       
   

3. Check Standard Deviation Proportion: Ensure the standard deviation is a fraction between 0.00 and 1.00.

Conclusion

By following these steps, you can effectively use SSPACE Basic to scaffold your genome assemblies, improving the contiguity and quality of your genome sequence. This guide provides a detailed walkthrough to ensure you can run SSPACE Basic successfully, from installation to execution. Happy scaffolding!

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Feel free to customise this blog post according to your preferences or add any additional details specific to your setup. Let me know if you have any questions or need further assistance!