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.
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Use github submodule for including other tools. #68
Currently parsnp uses prebuilt binaries for harvest, fasttree, and profile. For debugging-purposes and to make sure the code is always updated without having to update binaries, we should be including the repositories themselves and building them too.
Currently parsnp uses prebuilt binaries for harvest, fasttree, and profile. For debugging-purposes and to make sure the code is always updated without having to update binaries, we should be including the repositories themselves and building them too.