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.
The interval for each xmfa record is now inclusive, following the xmfa format. This only effects the internal coordinate representation, used by gingr. The s[seq_idx]:p[position] coordinates remain unchanged.
tqdm logging has been redirected to the Parsnp logger
The extension module now also uses SPOA and should work on multi-contig inputs. However, it is still experimental.
Extension is much more conservative than before, but still can produce less conserved alignments
s[seq_idx]:p[position]
coordinates remain unchanged.tqdm
logging has been redirected to the Parsnp logger