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.
--partition
flag, which splits recruited genomes into partitions of size--partition-size
(default 100).--no-recruit
option which skips the recruitment step, but still drops genomes if their size differs substantially from the reference.--min-ref-cov
option (default 90), which when used with--use-ani
, removes query genomes that do not cover at least 90% of the reference.