Haplotag 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.

mamba 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:

mamba install -c conda-forge bioconda::harpy

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

mamba install -n envname -c conda-forge bioconda::harpy

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Update

mamba 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

🌈 Get 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 single cent!