Get number of unique SNPs identified for each strains

[ShriramHPatel]

Hi,

I was able to generate reference based SMEG database utilizing -e flag in smeg build_species command. I have a few related doubts.

A) Is it possible to get number of unique SNPs (and position) identified for each strains after generating species database.

B) And in the next step of growth estimation, we are suppose to provide list of strains (as -g flag) for which we want to measure growth rate from metagenomic samples. In that case, whether number of SNPs used for growth rate measurements (using -m 1 flag) differ based on the strains included in the -g arguments or it will always be the same and unique for a particular strain in the database irrespective of the strains included in the -g arguments? To make it more clear, in a case when I have included 1 strain Vs 2 strains as a list to -g argument, would number of SNPs used for replication rate measurement will differ or will it be relative to the strains included in the -g arguments?

Please let me know if i am not clear enough or my understanding is not correct.

Regards,

Shriram

[aemiol]

A. No. Because Unique SNPs are determined only from the strains supplied using the -g flag. So the SNPs would be dependent on the strains of interest

[ShriramHPatel]

Thanks for your swift reply.

So in a scenario where strain of interest is just a single strain, would you recommend going with reference based estimation or denovo estimation?

because in reference based estimation with just one strain passing in -g flag, I have noticed very high number of SNPs used as non-zero SNP sites for growth rate estimation (in resulting file from growth estimation).

[aemiol]

If you pass a single strain with the -g flag, every nucleotide in the core genes will be used to estimate growth rate

[ShriramHPatel]

thanks again for your helpful reply.