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 (about 2 years ago)
• Default Branch: main
• Last Pushed: 2024-12-03T16:46:50.000Z (2 months ago)
• Last Synced: 2024-12-03T17:48:32.276Z (2 months ago)
• Topics: bioinformatics, haplotype, linked-reads, pipeline, sequencing, variant-calling
• Language: Python
• Homepage: https://pdimens.github.io/harpy
• Size: 399 MB
• Stars: 14
• Watchers: 2
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• 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&logo=hackthebox&logoColor=ffffff)](https://github.com/pdimens/harpy/releases)

[![documentation badge](https://img.shields.io/badge/read%20the-documentation-fbab3a?style=for-the-badge&logo=searxng&logoColor=ffffff)](https://pdimens.github.io/harpy) 

[![Anaconda-Server Badge](https://img.shields.io/conda/dn/bioconda/harpy.svg?style=for-the-badge&logo=docusign&logoColor=ffffff)](https://anaconda.org/bioconda/harpy)

[![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/pdimens/harpy/tests.yml?style=for-the-badge&logo=cachet&logoColor=ffffff)](https://www.youtube.com/watch?v=F1qdBPlK9M4)

[Haplotagging](https://doi.org/10.1073/pnas.2015005118) Data Processing Pipeline. Getting you from raw reads to assemblies, genotypes, or phased haplotypes or your 💰 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

conda 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

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

```

---

## Update

```bash

conda update -c conda-forge bioconda::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

```

## 🌈 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/).