Whole Genome Snp And Core Genome Snp

Question

[HG]

Hi everyone although this question posted earlier but due to not satisfactory result i am posting again as i want to do same kind of research:

"What are different ways (tools or online resources) to find SNPs between Whole Genomes of two Bacterial Strains?"

I have 50 ecoil whole genome sequence data. I already assembled all the sequence data and now i want to find SNP with a reference. Can anyone suggest some idea??

Thank you advance.

Answer 1

[Chrispin Chaguza]

You could use snp_sites to find polymorphic sites (SNPs) in your whole genome alignments https://github.com/sanger-pathogens/snp_sites.

I have created a basic analysis pipeline (http://mcgp.sourceforge.net/) that create alignments based on the whole genome content that's conserved between all strains and identifies all variation (SNPs) using the inferred 'core genome'. The could later be used to create phylogenetic trees at species level for 'bacterial' species.

If you have assemblies already, all you would need to do is order them using abacas to create one pseudo genome for each isolates. These ordered sequences can be provided as inputs for the script.