SNP analysis between two bacterial genomes

Question

[namgyalwangstuklama]

I want to perform a SNP analysis between two bacterial genomes. which tool is best for doing so? please help...

[Charles Yin]

To analyze SNP between two bacterial genomes, you may use histogram plot. You can see my programs at https://github.com/cyinbox/NGS

[WouterDeCoster]

Hmmm, can you elaborate how do histograms contribute to SNP identification? It is also not clear how to use the tools you linked.

Answer 1

[Israel Barrantes]

Use programs that have been specifically made for bacterial genomes, like Breseq (from FASTQs) or Snippy (from either FASTAs or FASTQs). In the Breseq paper you'll find the reasons why it's wrong to use programs that do not natively support haploid genomes.

Answer 2

[Brian Bushnell]

BBMap's callvariants.sh natively supports haploid genomes; the default ploidy is 1. It's been used extensively tracking SNP evolution in mutant E.coli populations.