Jwebster89/Virsequel

Virsequel is a Python script for identifying viral sequences in RNA-seq data.

Virsequel

Virsequel is a Python script for identifying viral sequences in RNA-seq data. It uses a combination of adapter trimming, assembly and BLAST to identify and extract viral sequences from raw RNA-seq reads.

Requirements

To run Virsequel, you'll need the following software and data:

• Python 3
• BBMap
• MetaSPAdes
• Diamond and/or NCBI BLAST
• A database of viral reference sequences in nucl or prot format.

Installation

1. Clone the Virsequel repository from GitHub:

git clone https://github.com/Jwebster89/virsequel.git

2. Install the required software:

• Python 3: Follow the instructions for your operating system to install Python 3.
• BBMap: Download and install BBMap from the BBMap website.
• MetaSPAdes: Download and install MetaSPAdes from the MetaSPAdes GitHub page.
• Diamond: Download and install Diamond from the Diamond GitHub page
• NCBI BLAST: Download and install BLAST from NCBI's download page

3. Download a database of viral reference sequences for viral sequence identification. E.g.

wget https://ftp.ncbi.nih.gov/refseq/release/viral/viral.1.protein.faa.gz
wget https://ftp.ncbi.nih.gov/refseq/release/viral/viral.1.1.genomic.fna.gz

Usage

To use Virsequel, run the run_virsequel.py script with the following command-line arguments:

usage: run_virsequel.py [-c CONFIG] [-1 READ_1] [-2 READ_2] [-a ADAPTER] [-o OUTPUT] [-b] [-d DATABASE] [-h] [-t THREADS]

        Identify viral sequences in rna seq data 

    Version: 0.3.0


options:
  -c CONFIG, --config CONFIG
                        Path to configuration file

Required Arguments:
  -1 READ_1, --read_1 READ_1
                        Forward RNA fastq.gz data
  -2 READ_2, --read_2 READ_2
                        Reverse RNA fastq.gz data
  -a ADAPTER, --adapter ADAPTER
                        adapter file for bbduk trimming
  -o OUTPUT, --output OUTPUT
                        output path
  -b, --blastn          run blastn instead of diamond blastx
  -d DATABASE, --database DATABASE
                        the path of the database to use for blast

Optional Arguments:
  -h, --help            show this help message and exit
  -t THREADS, --threads THREADS
                        Number of threads for non-spades processes

Virsequel will generate trimmed reads and meta RNA assemblies in the specified output directory and then perform a BLASTn or BLASTx based on user input

License

Virsequel is released under the GNU General Public License v3.0. See the LICENSE file for more information.

Contributing

If you find a bug or have a feature request, please create an issue on the GitHub repository. If you'd like to contribute code, please fork the repository and create a pull request with your changes.

Credits

Virsequel was created by John Webster.