Alvoc

Abundance learning for variants of concern

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Documentation

Overview

Alvoc is a tool for estimating the abundace of variants of concern from wastewater sequencing data. Its predecessor is Alcov, an abundance learning tool for SARS-CoV-2 variants.

In addition alvoc can also be used for:

• Determining the frequency of mutations of interest in BAM files
• Converting nucleotide and amino acid mutations for a particular virus
• Comparing amplicon GC content with its read depth (as a measure of degredation)

Installation

With Pip

Pip is the default package installer for Python.

1. Install Python. We recommend using pyenv for python version management.

2. Install the latest version from pypi.

pip install alvoc

With UV

UV is a fast, all-in-one Python tool for dependency, version, and project management, replacing pip, poetry, and more.

1. Install UV.
2. Install the latest version from pypi.

uv add alvoc

Yes, including a Docker image under the installation section makes sense, especially for users who prefer containerized environments or need to integrate your tool into CI/CD pipelines. Here's how you can include it:

With Docker

For users who prefer containerized environments, an official Docker image is available on GitHub Container Registry (GHCR).

1. Ensure you have Docker installed and running.
2. Pull the latest Docker image:

docker pull ghcr.io/alvoc/alvoc:latest

3. Run the container:

docker run --rm -it ghcr.io/alvoc/alvoc:latest

What is Alvoc?

Alvoc is a command-line tool designed to analyze viral sequencing data with a focus on identifying variants of concern and their defining mutations. With the ongoing rise of infectious diseases like SARS-CoV-2, monitoring and understanding viral evolution has become critical for researchers, public health officials, and laboratories.

Why Use Alvoc?

1. Lineage Identification

   • Alvoc helps determine which viral lineages are present in your sequencing data. For example, it can identify emerging lineages like B.1.1.7 (Alpha) or P.1 (Gamma) for SARS-CoV-2.
   • Use Alvoc when you need to:
     • Compare samples to known lineage-defining mutations.
     • Detect specific lineages in samples from an outbreak.
     • Include or exclude specific lineages (whitelisting/blacklisting).

2. Mutation Detection

   • Alvoc allows you to detect mutations in sequencing data with customizable depth thresholds.
   • Use this feature to:
     • Find known or novel mutations in viral samples.
     • Focus on specific mutations like S:N501Y or E484K that are critical for vaccine efficacy or transmissibility.

3. Amplicon Quality Assessment

   • Viral sequencing often relies on amplicon-based approaches. Alvoc provides tools to assess amplicon metrics like coverage and GC content.
   • This helps ensure high-quality sequencing data for downstream analyses.

When to Use Alvoc?

You should use Alvoc if you are:

• A researcher analyzing viral sequencing data to study genetic variation and evolution.
• A public health analyst monitoring variants of concern during outbreaks.
• A bioinformatician processing large-scale sequencing data to identify mutations and lineages.
• A laboratory scientist validating amplicon-based sequencing data for accuracy.

Alvoc simplifies these workflows into a set of streamlined commands, saving time and improving consistency across analyses.

License

This project is licensed under the terms of the MIT license.