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.
evezeyl opened this issue · comments
Hi,
That would be nice to have an option to fix the seed for testing purposes and reproducibility between tools implemented in different platforms/pipelines where parsnp is used.
Best regards
Eve
Hi @evezeyl,
We just released a new version of Parsnp that should fix this issue. Please let me know if you continue to see non-deterministic results with version 2.0.0.