https://github.com/pdimens/harpy
Process linked-read data, from raw sequences to phased haplotypes, batteries included. Works with WGS too!
https://github.com/pdimens/harpy
bioinformatics haplotype linked-reads pipeline sequencing variant-calling
Last synced: 3 months ago
JSON representation
Process linked-read data, from raw sequences to phased haplotypes, batteries included. Works with WGS too!
- Host: GitHub
- URL: https://github.com/pdimens/harpy
- Owner: pdimens
- License: gpl-3.0
- Created: 2022-11-18T17:51:21.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2026-02-02T21:22:35.000Z (3 months ago)
- Last Synced: 2026-02-03T10:57:43.987Z (3 months ago)
- Topics: bioinformatics, haplotype, linked-reads, pipeline, sequencing, variant-calling
- Language: Python
- Homepage: https://pdimens.github.io/harpy
- Size: 476 MB
- Stars: 18
- Watchers: 1
- Forks: 2
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
- awesome-linked-reads - Harpy - commit/pdimens/harpy?label=%20) (Tools)
README
[](https://pdimens.github.io/harpy)
[](https://github.com/pdimens/harpy/releases)
[](https://pdimens.github.io/harpy)
[](https://www.youtube.com/watch?v=F1qdBPlK9M4)
[](https://www.fml.tuebingen.mpg.de/9418/haplotagging)
[Linked-read](https://doi.org/10.1073/pnas.2015005118) 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](https://pdimens.github.io/harpy/install/).
### 🐍 Conda
```bash
conda create -n harpy -c bioconda -c conda-forge harpy
conda activate harpy
```
### 🌟 Pixi
```bash
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
```bash
docker pull quay.io/biocontainers/harpy
```
#### 🅰️ Apptainer
Find the most recent tag [here](https://quay.io/repository/biocontainers/harpy?tab=tags) and replace `$TAG` with it or use the `TAG=$(curl ...)` part below to pull the latest version name using the repository's API.
```bash
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.
```bash
harpy module options... args...
```
## 🌈 Getting Started
No data? No problem! Use [HACk](https://davidebolo1993.github.io/visordoc/usecases/usecases.html#visor-hack) to simulate genomic variants from an existing genome and use [Mimick](https://pdimens.github.io/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](https://pdimens.github.io/LRInversionSimulations/).
## 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](https://pubmed.ncbi.nlm.nih.gov/40575478/). PMID: 40575478; PMCID: PMC12198493.