AI Article Synopsis
- ipyrad is a free, open-source tool for assembling and analyzing restriction site-associated DNA sequences, suitable for both de novo and reference-based approaches.
- It is built to handle large datasets, efficiently managing hundreds of taxa and thousands of samples, and supports parallel processing on high-performance computing systems.
- ipyrad is accessible as a command line tool or a Python package, with comprehensive online documentation and tutorials available, allowing users to create complex, reproducible scripts for further analysis.
Article Abstract
Summary: ipyrad is a free and open source tool for assembling and analyzing restriction site-associated DNA sequence datasets using de novo and/or reference-based approaches. It is designed to be massively scalable to hundreds of taxa and thousands of samples, and can be efficiently parallelized on high performance computing clusters. It is available both as a command line interface and as a Python package with an application programming interface, the latter of which can be used interactively to write complex, reproducible scripts and implement a suite of downstream analysis tools.
Availability And Implementation: ipyrad is a free and open source program written in Python. Source code is available from the GitHub repository (https://github.com/dereneaton/ipyrad/), and Linux and MacOS installs are distributed through the conda package manager. Complete documentation, including numerous tutorials, and Jupyter notebooks demonstrating example assemblies and applications of downstream analysis tools are available online: https://ipyrad.readthedocs.io/.
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Article Synopsis
- ipyrad is a free, open-source tool for assembling and analyzing restriction site-associated DNA sequences, suitable for both de novo and reference-based approaches.
- It is built to handle large datasets, efficiently managing hundreds of taxa and thousands of samples, and supports parallel processing on high-performance computing systems.
- ipyrad is accessible as a command line tool or a Python package, with comprehensive online documentation and tutorials available, allowing users to create complex, reproducible scripts for further analysis.
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