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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Recombination filtering and default parameters #66
Hi, I have a quick question about the analyses performed for the Harvest Suite paper: was recombination filtering (-x) used? Further, is there a reason that this is not enabled by default? From the paper, it sounds like the recombination filtering is part of the workflow, but I haven't been able to find any indication here or on the website as to which parameters were used for those analyses, or why that is not a default.
Hi, I have a quick question about the analyses performed for the Harvest Suite paper: was recombination filtering (
-x) used? Further, is there a reason that this is not enabled by default? From the paper, it sounds like the recombination filtering is part of the workflow, but I haven't been able to find any indication here or on the website as to which parameters were used for those analyses, or why that is not a default.Thanks in advance, and thanks for a great tool!