Calling Snps In Multiple Species

Question

[Mark]

Hi

Does anyone know of a tool that calls for SNPs in multiple species. I have two related species and a few strains of each species. I like to construct a SNP phylogeny to see the relationship between these species according to the SNP differences.

I know that cannot be achieved using samtools mpileup as it calls for SNPs in multiple strains of the same species but not multiple species.

Thanks in advance.

Mark

Answer 1

[Zam Iqbal]

Hi. Yes, Cortex (specifically the cortex_var executable) should be able to do this (I have done it between chimp and human, and between strains of microbes). Essentially you do multiple genome assemblies simultaneously, and find variants directly, without building a reference.

The paper can be found here: http://dx.doi.org/10.1038/ng.1028 and the software here: http://cortexassembler.sourceforge.net/index_cortex_var.html

It does depend a little bit on the size of the genome as to how many strains you can compare at a time, and also their level of divergence. But if your genome is ~10Mb, then you ought to be able to compare many hundreds. If it's around human-size, then you start to need large memory machines (10 humans need about 56Gb of RAM).

regards

Zam

[Zam Iqbal]

oops - I apologise for a type in my last comment. 10 humans need 256Gb of RAM not 56Gb of RAM