snippy VS RagTag

This should be of help, if you think you can get have a decent (closely related) reference genome from NCBI: https://github.com/tseemann/snippy

snippy is a nice tool for this!

So, let's say I have a batch of 20 samples, and I found evidence for my genus of interest in 5. What I've done is used Snippy (https://github.com/tseemann/snippy) with mapping based on a reference species in the genus. Snippy finds shared "core" regions of the reference species that are present in all samples and compares the SNPs between the samples. I find that each sample has distinct SNPs, which I believe indicates that the bacteria in each sample are not the same isolate. Thus, I am trying to argue that the bacteria could not have come from a shared contamination event during library prep. Does this make things more clear?

My first idea was to assemble the contigs into scaffolds (e. g. using RagTag) and then look for a tool that can identify these mutations. However, I've also come across snippy, which is a tool that can identify mutations from reads. I don't know if I can just apply it to contigs though (probably not).

I would use snippy for this if there references are haploid genomes https://github.com/tseemann/snippy

[18:37:12] Obtained from https://github.com/tseemann/snippy

Has anyone used ragtag to correct bacterial assemblies (https://github.com/malonge/RagTag/wiki/correct) ? Is it helpful?

Use ragtag. https://github.com/malonge/RagTag

RagTag. Not sure how well it works for small genomes.

My first idea was to assemble the contigs into scaffolds (e. g. using RagTag) and then look for a tool that can identify these mutations. However, I've also come across snippy, which is a tool that can identify mutations from reads. I don't know if I can just apply it to contigs though (probably not).