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Assnake Metagenomic Analysis System

Overview

Assnake is a comprehensive metagenomics analysis tool designed for short read sequencing data, focusing on microbiome studies. It combines various bioinformatics tools into an integrated workflow for metagenomic data processing and analysis.

Key Features

  • Dataset and Sample Management: Organizes datasets and individual biological samples.
  • Modular Preprocessing and Analysis: Customizable preprocessing and analysis steps tailored to specific research needs.
  • Preset Management: Ensures consistent and reproducible analyses through preset configurations.
  • Command Line Interface (CLI): User-friendly CLI for easy access to functionalities.

System Architecture

Assnake's architecture is centered around datasets containing unique samples. Each sample can go through several preprocessing stages, captured as SampleContainers. Pipelines manage the workflow, applying various Results and Presets for analysis.

Installation

  1. Create a Conda Environment: (Recommended to manage dependencies)

    conda create -n assnake_env python=3.10

  2. Activate your new Conda Environment:

    conda activate assnake_env

  3. Clone the Repository:

    git clone https://github.com/ASSNAKE/assnake.git

  4. Navigate to the Repository and Install:

    cd assnake
pip install -e ./

  5. Initialize Assnake Configuration:

    assnake config init

    It will ask you to specify the folder for assnake database. This can grow quite large (10Gb +) due to the conda envs that will be installed into this folder, so choose wisely, contact your system administrator if you are unsure about the directory choice.

Quick Start

  • To create and manage datasets: assnake dataset <command>
  • To import sequencing data: assnake dataset import-reads
  • To execute analysis pipelines: assnake result <analysis-command>

Documentation

Detailed documentation, including usage guidelines and advanced configurations, is available in the docs directory. Examples and tutorials are provided for guidance.

Contributing

Contributions to Assnake are welcome, including documentation improvements, new features, and bug reporting. Please refer to the contributing guidelines for more information.

License

Assnake is open-source software, available under the MIT License. See LICENSE.txt for details.

Support and Contact

For support or inquiries, please open an issue on the GitHub repository or contact fedorov.de@gmail.com.

Note: This README offers a general overview of the Assnake system. For comprehensive information, refer to the individual documentation files within the repository.