enhancement : option to fix seed

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.

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enhancement : option to fix seed #138

Closed evezeyl closed 6 months ago

evezeyl commented 6 months ago

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

bkille commented 6 months ago

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.