Journal
BIOINFORMATICS
Volume 36, Issue 8, Pages 2592-2594Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btz966
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Funding
- National Science Foundation [DEB-1253710, DEB 1745562, DEB-1557059]
- Sao Paulo Research Foundation [BIOTA] [2013/50297-0]
- National Aeronautics and Space Administration through the Dimensions of Biodiversity Program [DOB 1343578]
- Graduate Center of the City University of New York
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A 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.
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