Linked-read data processing pipeline. Getting you from raw linked reads to assemblies, genotypes, or phased haplotypes. Batteries included 🔋

✨ Now works with TELLseq, stLFR, and non-linked read data! ✨

📥 Install

Detailed installation instructions are described in the documentation.

🐍 Conda

conda create -n harpy -c bioconda -c conda-forge harpy
conda activate harpy

🌟 Pixi

pixi global install -c conda-forge -c bioconda harpy
# or locally #
pixi init -c conda-forge -c bioconda projectname && cd projectname && pixi add harpy

📦 Containers

🐳 Docker

docker pull quay.io/biocontainers/harpy

🅰️ Apptainer

Find the most recent tag here and replace $TAG with it or use the TAG=$(curl ...) part below to pull the latest version name using the repository's API.

TAG=$(curl -s "https://quay.io/api/v1/repository/biocontainers/harpy/tag/" | cut -d'"' -f6)
apptainer pull docker://quay.io/biocontainers/harpy:$TAG

⚡ Usage

Just call harpy or harpy --help on the command line to get started! If installed via container, then call the containerized-Harpy however you are used to using containers on your system.

harpy module options... args...

🌈 Getting Started

No data? No problem! Use HACk to simulate genomic variants from an existing genome and use Mimick to create linked-read data from an existing genome! You can see what haplotagging (or other linked read) data and Harpy are like without investing a single cent! A real-world walkthrough of how we did this for a benchmarking experiment can be found here.

Citation

Dimens PV, Franckowiak RP, Iqbal A, Grenier JK, Munn PR, Therkildsen NO. Harpy: a pipeline for processing haplotagging linked-read data. Bioinform Adv. 2025 Jun 5;5(1):vbaf133. doi: 10.1093/bioadv/vbaf133. PMID: 40575478; PMCID: PMC12198493.