Call SNP

[crayfish]

Hi,everyone, I have two samples (A and B) they are the same species with different phenotype, I got 454 transcriptome data for both of them, I want to detect the SNP between A and B, means I want to find some SNPs that can distinguish A and B, I do not have reference genome, so I use the de novo transcriptome assemble as reference. so can you suggest some software that i can use?

thank you

[nucleus]

Take a look at Cortex (http://cortexassembler.sourceforge.n...ortex_var.html), I think it can be used without a reference,

[crayfish]

Thank you, i will try it