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Parsnp

Rapid core genome multi-alignment

Project home page: https://github.com/marbl/parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

Contents:

.. toctree::
   :maxdepth: 3

   parsnp/quickstart
   parsnp/components
   parsnp/installation
   parsnp/paramaters
   parsnp/tutorial
   parsnp/faq
   parsnp/source
   parsnp/citation
   parsnp/license

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