https://github.com/pdimens/harpy
Process haplotagging data, from raw sequences to phased haplotypes, batteries included.
https://github.com/pdimens/harpy
bioinformatics haplotype linked-reads pipeline sequencing variant-calling
Last synced: 6 months ago
JSON representation
Process haplotagging data, from raw sequences to phased haplotypes, batteries included.
- Host: GitHub
- URL: https://github.com/pdimens/harpy
- Owner: pdimens
- License: gpl-3.0
- Created: 2022-11-18T17:51:21.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2025-04-07T19:38:05.000Z (6 months ago)
- Last Synced: 2025-04-07T20:36:30.642Z (6 months ago)
- Topics: bioinformatics, haplotype, linked-reads, pipeline, sequencing, variant-calling
- Language: Python
- Homepage: https://pdimens.github.io/harpy
- Size: 452 MB
- Stars: 16
- Watchers: 2
- Forks: 2
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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.fml.tuebingen.mpg.de/9418/haplotagging)
[](https://www.youtube.com/watch?v=F1qdBPlK9M4)
[Haplotagging](https://doi.org/10.1073/pnas.2015005118) Data Processing Pipeline. Getting you from raw linked-reads to assemblies, genotypes, or phased haplotypes. Batteries included 🔋.
## 📥 Install
### 🐍 Conda
It's best to create a new environment for a harpy installation. The code below creates a new conda/mamba environment called `harpy` (via `-n harpy`) and installs harpy into it. You can name this environment whatever you like using the `-n somename` argument.
```bash
conda create -n harpy -c bioconda -c conda-forge harpy
```
Once conda/mamba finishes, activate the harpy conda/mamba environment with:
```bash
conda activate env_name
```
where `env_name` is the name of that environment. After doing so, the `harpy` executable should be callable from your path.
⬇️ install as local conda environment
Alternatively, you can create the environment locally within a specific project folder, just swap `-n harpy` for
`-p path/to/workdir/harpy`, which creates the environment in that specific folder (e.g. `potato_blight/harpy`).
```
# for local project directory
conda create -p path/to/workdir/harpy -c bioconda -c conda-forge harpy
```
⬇️ install into existing conda environment
If you wish to install harpy and its dependencies into an existing environment, activate that environment (`conda activate env_name`) and execute this installation code:
```bash
conda install -c conda-forge bioconda::harpy
```
Or provide `-n envname` to install it into an existing environment named `envname`
```bash
conda install -n envname -c conda-forge bioconda::harpy
```
⬆️ updating harpy
If installed via conda, you can update Harpy by activating the environment
and running `conda update` like so:
```bash
conda update -c conda-forge bioconda::harpy
```
### 🌟 Pixi
If you prefer [Pixi](https://pixi.sh/latest/) (it's pretty good, you should try it), you can
install Harpy to be accessible in your PATH:
🌟 how to install pixi
```bash
# install pixi
curl -fsSL https://pixi.sh/install.sh | bash
# add this to ~/.zshrc or ~/.bashrc (or equivalent)
export PATH=~/.pixi/bin:$PATH
```
```bash
pixi global install -c conda-forge -c bioconda harpy
```
⬇️ install harpy into local environment
Likewise, you can do an installation into a local project directory:
```bash
pixi init -c conda-forge -c bioconda projectname && cd projectname
pixi add harpy
```
After that finishes, you can activate the environment with:
```bash
pixi shell
```
Or run `harpy` by prefixing it with `pixi run`:
```bash
pixi run harpy
```
⬆️ updating harpy
If installed via Pixi, you can update Harpy with `pixi update`:
```bash
# global install
pixi global update harpy
# local install
# project dir has the pixi.toml file
cd path/to/projectdir
pixi update harpy
```
## ⚡ Usage
Just call `harpy` or `harpy --help` on the command line to get started!
```bash
harpy
```
## 🌈 Getting Started
No data? No problem! Harpy lets you [simulate genomic variants](https://pdimens.github.io/harpy/workflows/simulate/simulate-variants/)
from an existing genome and can also [create haplotag data](https://pdimens.github.io/harpy/workflows/simulate/simulate-linkedreads/)
from an existing genome! You can see what haplotag data (and Harpy) are like without paying a cent! A simple tutorial on simulating
both of these can be found [here](https://pdimens.github.io/harpy/blog/simulate_diploid/).