Haplotagging 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.

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

⚪️ install into an existing conda environment ⚪️

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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

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Update

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

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!

harpy

🌈 Getting Started

No data? No problem! Harpy lets you simulate genomic variants from an existing genome and can also create haplotag data 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.