Test VIRULIGN as a substitute to Advanced Genome Aligner

[victor5lm]

Background

Advanced Genome Profiler (AGA) is a software tool used by Genome Detective (a software that is similar to PikaVirus) for multiple sequence alignment and analysis, often employed in genomics to align coding sequences (CDS) while preserving their reading frames. AGA is known for its performance in handling large datasets and providing in-depth genome profiling. However, AGA is not a free tool and is private, making it unsuitable for users who require open-source and freely available alternatives.

VIRULIGN, on the other hand, is a fast and open-source alignment and annotation tool for protein coding sequences of closely-related viruses, based on reference genomes. Since COATi is open-source and freely available, it could be used to replace AGA.

This issue aims to test whether VIRULIGN can effectively substitute AGA, by evaluating its features, installation process, and compatibility with existing workflows.

Objective

Evaluate whether VIRULIGN can effectively replace Advanced Genome Profiler (AGA) in the context of genome alignment and analysis. This task involves testing VIRULIGN for its installation, functionality, compatibility, and performance as an alternative to AGA.

Tasks

Installation Check

• Verify if VIRULIGN can be installed on the corresponding environment (e.g., local machines, HPC clusters).
• Check whether VIRULIGN is available as a Singularity/Docker image.
• Assess if there are any dependencies or installation aspect that must be considered.

Input Requirements

• Identify and document the input file formats VIRULIGN accepts (e.g., FASTA, GenBank, etc.).
• Determine if any specific preprocessing of input sequences is needed.

Output Generation

• Investigate the types of output VIRULIGN generates.
• Ensure that the output can be easily integrated into downstream analysis pipelines.

Functional Testing

• Run VIRULIGN with test data to evaluate its performance and results.
• For the wrap-up part, please present the most remarkable aspects from this process.

Execution Process

• During the wrap-up session, please present the steps for launching VIRULIGN, including necessary command-line arguments or configuration files.
• Check whether the software is user-friendly and well-documented.
• Assess whether the tool requires additional setup (e.g., environment variables, configuration files).

Maintenance and Support

• Evaluate if the software is being actively maintained (check for recent updates, issues, pull requests).
• Look for documentation and community support (e.g., GitHub issues, forums, mailing lists).

Expected Outcome

A comprehensive assessment of VIRULIGN as a potential replacement for Advanced Genome Profiler, including installation and execution details, input/output formats, functional performance, and compatibility with existing workflows.

[Leti3pa]

I tried using Virulign with both some viral contigs and its reference genome in FASTA format, but it didn't work as expected. I then attempted to convert the GenBank XML file of the virus into a format compatible with Virulign, but encountered an issue with an ORF that needed to be joined, which complicated the process. Afterwards, I tested an example from the GitHub repository and noticed that the input sequences were complete genomes, and the applications appeared to focus primarily on mutations. Given that my input consists of contigs, I don't think this tool is suited for this application