This is a collection of tools for NGS data analysis. It provides many easy-to-use functionalities to clean, visualize, and analyze NGS results.
Latest atgtools version:
pipx installs Python applications in isolated environments:
pipx install atgtoolsuv pip install atgtoolsFor 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 --helpThe package provides tools for both alpha and beta diversity analysis.
Calculate various alpha diversity indices:
- Shannon (natural log and custom base)
- Gini-Simpson
- Simpson
- Dominance
- Richness
- Pielou's Evenness
atg div alpha --input abundance.tsvCalculate dissimilarity between samples using various metrics:
- Bray-Curtis
- Jensen-Shannon
- Jaccard
- Euclidean
- UniFrac (weighted and unweighted)
atg div beta --input abundance.tsv --metric braycurtisCheck 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
Create manifest files for QIIME2:
atg tools manifest --fastq_dir /path/to/fastq --output manifest.tsvSupported FASTQ naming schemes:
sample_R1.fastq.gzsample_R2.fastq.gzsample_S01_R1.fastq.gzsample_S01_R2.fastq.gz
atg tools oneliner: Convert multiline FASTA to single lineatg tools countfq: Count reads in FASTQ filesatg tools abundance: Generate relative abundance tablesatg tools download: Download ENA dataatg tools retrieve: Search and retrieve ENA dataatg tools search: Search ENA database