ATGtools

This is a collection of tools for NGS data analysis. It provides many easy-to-use functionalities to clean, visualize, and analyze NGS results.

Installation

Latest atgtools version:

Recommended Installation Methods

Using pipx (Recommended)

pipx installs Python applications in isolated environments:

pipx install atgtools

Using uv (Alternative)

uv pip install atgtools

Development Setup

For development, clone the repository and set up the environment using uv:

# Clone the repository
git clone https://github.com/yourusername/atgtools.git
cd atgtools

# Create and activate virtual environment with Python 3.12
uv venv --python 3.12
source .venv/bin/activate  # On Unix/macOS

# Install dependencies
uv sync

# Use as a module
python -m atg --help

Features

Diversity Analysis

The package provides tools for both alpha and beta diversity analysis.

Alpha Diversity

Calculate various alpha diversity indices:

• Shannon (natural log and custom base)
• Gini-Simpson
• Simpson
• Dominance
• Richness
• Pielou's Evenness

atg div alpha --input abundance.tsv

Beta Diversity

Calculate dissimilarity between samples using various metrics:

• Bray-Curtis
• Jensen-Shannon
• Jaccard
• Euclidean
• UniFrac (weighted and unweighted)

atg div beta --input abundance.tsv --metric braycurtis

Utility Tools

Git Repository Management

Check multiple git repositories in one pass:

atg tools git [options]

Options:

• --verbose/-v: Show files & commits
• --remote/-r: Force remote update
• --untracked/-u: Show untracked files
• --dir/-d: Search specific directory for repositories
• --all-branch/-a: Show status of all branches
• --stash/-s: Show stashed changes

Manifest Creation

Create manifest files for QIIME2:

atg tools manifest --fastq_dir /path/to/fastq --output manifest.tsv

Supported FASTQ naming schemes:

• sample_R1.fastq.gz
• sample_R2.fastq.gz
• sample_S01_R1.fastq.gz
• sample_S01_R2.fastq.gz

Other Tools

• atg tools oneliner: Convert multiline FASTA to single line
• atg tools countfq: Count reads in FASTQ files
• atg tools abundance: Generate relative abundance tables
• atg tools download: Download ENA data
• atg tools retrieve: Search and retrieve ENA data
• atg tools search: Search ENA database