I'm approaching a dna mutation analysis for the first time. I have dna sequences of a structural gene (454 reads, about 450 bp, single end) sequenced in 10 samples and I need to find mutations and quantify the abundance of each mutant in each sample.
This is how I'm thinking to proceed:
-demultiplexing sequences using qiime
-trimming low quality bases and filtering reads too short
-clustering them at 100% similarity using usearch
-aligning centroids to some sequences found at NCBI using mummer
My questions are:
first of all, is my approach correct? Do anybody has experience in this kind of analysis and which approach used?
then, I don't know if mummer is the good choice... It is designed for snp discover in genomes, so I don't know if it could be a good idea using it for sequences that I expect to be very similar among them. If not, any other suggestion about softwares to use?