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.
All dependency tools must be on the system path (no longer defaults to bin/)
More robust error checking (skips bad files instead of crashing, more warnings + debug mode)
Fixed .gbk parsing
Convenient input now allows sequences to be supplied via regex i.e. what used to be parsnp -d ref/ -r ! is now parsnp -d ref/*.fna which allows for heterogeneous input directories and spread out data.
bin/)parsnp -d ref/ -r !is nowparsnp -d ref/*.fnawhich allows for heterogeneous input directories and spread out data.