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polyat

polyat is a command-line tool that scans FASTQ files for poly-A/T homopolymers typically derived from carrier RNA (such as those in the QIAamp Viral RNA Mini Kit). Each read is evaluated once; the tool reports how many reads contain ≥10, ≥15, or ≥20 identical A/T bases together with their relative percentages. The tool produces both a concise polyA_counts.txt QC table and an interactive polyA_report.html summary with per-column filters and a poly-A/T histogram.

Features

  • Accepts .fastq, .fastq.gz, .fq, and .fq.gz files
  • Streams data without decompressing entire files to disk
  • Counts each read at most once per length threshold (10/15/20 nt)
  • Writes a tab-separated summary table suitable for downstream QC

Installation

Prerequisites

First, install conda if you haven't already:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Option 1: Using Conda (Recommended)

Install Install polyat via Conda:

conda create -n polyat -c conda-forge -c bioconda polyat -y
conda activate polyat

Option 2: From Source Code

git clone https://github.com/DaanJansen94/polyat.git
cd polyat
pip install .

Usage

General command:

polyat -i /path/to/fastq_dir -o /path/to/output_dir

Arguments:

-i / --input   Required input directory containing FASTQ/FQ files
-o / --output  Required output directory (created if missing)

polyat always writes polyA_counts.txt inside the output directory, counting each read at most once per threshold (≥10/15/20 nt).

Citation

If you use polyat in your research, please cite:

Jansen, D., Laumen, J., Siebenmann, E., & Vercauteren, K. (2025). polyat: Poly-A/T summarization (v0.1.2). [https://doi.org/10.5281/zenodo.17640044](https://doi.org/10.5281/zenodo.17640044).

License

This project is licensed under the GNU General Public License v3.0 (GPL-3.0) - see the LICENSE file for details.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

Support

If you encounter any problems or have questions, please open an issue on GitHub.