Imagine you have a whole genome shotgun (WGS) sequence of a bacterium. You want to identify what species it is, based on this genome sequence, but various softwares give different results. Which software would you trust the most and why ? Preferably, choose between RAST, PATRIC-BRC, KmerFinder and TYGS, please.
Barbara Brezna The case when various softwares assign WGS draft genome to different species is rather usual for new species with small difference. Even choice of variable settings (like analysis of draft genome vs. complete genome data) within the same program can give you different species identification.
It is recommended to use the core genome analysis with three different approaches: "core-genome SNP typing based on read mapping, k-mer analyses, and whole-genome alignment" (Treangen, T.J., Ondov, B.D., Koren, S. et al. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol 15, 524 (2014). https://doi.org/10.1186/s13059-014-0524-x).
I recomend GTDB-tk (https://github.com/Ecogenomics/GTDBTk), which is based on ANI tree versus a bacterial genomes database.
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