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https://github.com/pdimens/harpy

Process raw 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: about 2 months ago
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Process raw 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 (over 1 year ago)
Default Branch: main
Last Pushed: 2024-05-13T20:01:42.000Z (about 2 months ago)
Last Synced: 2024-05-13T21:24:49.195Z (about 2 months ago)
Topics: bioinformatics, haplotype, linked-reads, pipeline, sequencing, variant-calling
Language: Python
Homepage: https://pdimens.github.io/harpy
Size: 386 MB
Stars: 9
Watchers: 1
Forks: 1
Open Issues: 3
Metadata Files:
- Readme: README.md
- License: LICENSE

Lists

awesome-linked-reads - HARPY - commit/pdimens/harpy?label=%20) (Tools)

README

[![logo](https://github.com/pdimens/harpy/blob/docs/static/logo_trans.png?raw=true)](https://pdimens.github.io/harpy)

![GitHub Release](https://img.shields.io/github/v/release/pdimens/harpy?style=for-the-badge)
[![documentation badge](https://img.shields.io/badge/read%20the-documentation-fbab3a?style=for-the-badge&logo=Read%20The%20Docs)](https://pdimens.github.io/harpy)
[![Anaconda-Server Badge](https://img.shields.io/conda/dn/bioconda/harpy.svg?style=for-the-badge)](https://anaconda.org/bioconda/harpy)

[Haplotag](https://doi.org/10.1073/pnas.2015005118) Data Processing Pipeline. Getting you from raw reads to genotypes/phased haplotypes or your money back.

## 📥 Install
To avoid dependency conflicts with an existing environment, it is 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
mamba create -n harpy -c bioconda -c conda-forge harpy
```

⚪️ install into an 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
mamba install -c bioconda -c conda-forge harpy
```
Or provide `-n envname` to install it into an existing environment named `envname`
```bash
mamba install -n envname -c bioconda -c conda-forge harpy
```

---

## 🌟 Activate the harpy environment
Once conda/mamba finishes, activate the conda/mamba environment you installed harpy into 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.

## ⚡ Usage
Just call `harpy` or `harpy --help` on the command line to get started!
```bash
harpy
```