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.
bkille
commented
4 years ago
https://github.com/marbl/parsnp/blob/63bea137e2726c860133f0b97da688dab3c1b92b/Parsnp.py#L16
If a filename is valid on the filesystem, is there any need to re-validate?