What is the best tool/wrokflow for a core SNP alignment?

Question

[blur]

Hi,

I want to do a core SNP alignment based phylogenetic tree for bacterial species (haploids), and I have seen different papers relating tools and workflows. Can anyone recommend the best workflow for reliable SNP based alignment trees? I have seen Snippy in several papers - is that the most reliable tool?

Thank you

Answer 1

[Michael]

In the following comparison, snippy came out on top of over 200 pipelines averaging over different performance measures. This paper seems to be a good argument to defend its use.

Stephen J Bush, Dona Foster, David W Eyre, Emily L Clark, Nicola De Maio, Liam P Shaw, Nicole Stoesser, Tim E A Peto, Derrick W Crook, A Sarah Walker, Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines, GigaScience, Volume 9, Issue 2, February 2020, giaa007, https://doi.org/10.1093/gigascience/giaa007