pvga 0.0.2

PVGA is a powerful virus-focused assembler that does both assembly and polishing.

PVGA

Overview

PVGA is a powerful virus-focused assembler that does both assembly and polishing. For virus genomes, small changes will lead to significant differences in terms of viral function and pathogenicity. Thus, for virus-focused assemblers, high-accuracy results are crucial. Our approach heavily depends on the input reads as evidence to produce the reported genome. It first adopts a reference genome to start with. We then align all the reads against the reference genome to get an alignment graph. After that, we use a dynamic programming algorithm to compute a path with the maximum weight of edges supported by reads. Most importantly, the obtained path is used as the new reference genome and the process is repeated until no further improvement is possible.

Installation

To install and use PVGA, please follow these steps:

   sudo apt install blasr
   conda create -n pvga python=3.10
   conda activate pvga
   git clone https://github.com/SoSongzhi/PVGA.git
   cd PVGA
   pip install -r requirements.txt

Usage

To display the help message and see the available command-line options for the pvga.py script, run the following command in your terminal:

python pvga.py -h

To perform assembly using the pvga.py script, use the following command structure:

python pvga.py -r [reads location] -b [backbone locatino] -n [ITERATION NUM] -od [output dir]

Arguments

• -r [reads location], --reads [reads location]:
  Path to the input reads file or directory containing the sequencing reads (e.g., FASTQ or FASTA files).

• -b [backbone location], --backbone [backbone location]:
  Path to the backbone sequence file (e.g., a reference genome or plasmid in FASTA format).

• -n [ITERATION NUM], --iterations [ITERATION NUM]:
  Number of iterations to run the assembly process. This controls the depth or refinement of the assembly.

• -od [output dir], --output_dir [output dir]:
  Path to the directory where the output files (e.g., assembled sequences, logs, and reports) will be saved.

Example Command

python pvga.py -r hiv_30x_4k_id90_98_2.5.fastq -b HXB2.fa -n 10 -od test_pvga

License

This project is licensed under the MIT License. See the LICENSE file for more details.

Contact

For questions or support, please contact [[e-mail]] or open an issue on GitHub.