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

🐍 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.

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

Once conda/mamba finishes, activate the harpy conda/mamba environment with:

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:

conda install -c conda-forge bioconda::harpy

Or provide -n envname to install it into an existing environment named envname

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:

conda update -c conda-forge bioconda::harpy

🌟 Pixi

If you prefer Pixi (it's pretty good, you should try it), you can install Harpy to be accessible in your PATH:

🌟 how to install pixi

# install pixi
curl -fsSL https://pixi.sh/install.sh | bash

# add this to ~/.zshrc or ~/.bashrc (or equivalent) 
export PATH=~/.pixi/bin:$PATH

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:

pixi init -c conda-forge -c bioconda projectname && cd projectname
pixi add harpy

After that finishes, you can activate the environment with:

pixi shell

Or run harpy by prefixing it with pixi run:

pixi run harpy

⬆️ updating harpy

If installed via Pixi, you can update Harpy with pixi update:

# 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!

harpy

🌈 Getting Started

No data? No problem! Harpy lets you simulate genomic variants from an existing genome and can also create linked-read data from an existing genome! You can see what haplotagging (or other linked read) data and Harpy are like without paying a cent! A simple tutorial on simulating both of these can be found here.