Question

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

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2.1 years ago

blur ▴ 280

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

Gubbins snp-sites SNP-detector snippy SNP • 714 views

ADD COMMENT • link updated 2.1 years ago by Michael 55k • written 2.1 years ago by blur ▴ 280

score 1 · Answer 1 · 2022-10-26

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