Help with Finding SNPs in H. pylori Assembled Genomes

Question

[vrao]

Hey everyone,

I’m working with 1500 assembled Helicobacter pylori genomes and trying to identify SNPs using Snippy. My reference genome is Helicobacter pylori 26695, and I’m running the following commands:

snippy --outdir outdir_HP1 --ref ref.gbff --ctgs HP_1.fasta snippy --outdir outdir_HP2 --ref ref.gbff --ctgs HP_2.fasta

snippy-core outdir_HP1 outdir_HP2

However, I keep getting 0 variants in the output.

I’m specifically looking for variants in babA, vacA, hopQ genes.

Has anyone successfully used Snippy for SNP calling with assembled genomes rather than raw reads? How to troubleshoot why Snippy isn’t detecting any SNPs?

Thanks in advance!