Hi all. Apologies if my question is basic or my terminology isn't 100% right as I'm fairly new to the world of NGS.
Basically, I will have a library of, let's say 100,000 clones, each differing by a 100bp sequence. This 100bp section of the library will be randomly mutagenized to have a single random mutation (obviously this won't be possible and many clones will remain WT, and many will have more than one mutation).
What I'll then need to do is run this on MiSeq, and analyse it in a way that I know both the coverage of the new mutated library, as well as what percentage of the new library is mutated to the extent that I want (ie. a single mutation). I am not sure what tool I can use to align a fastq to 100,000 references, not to mention any analysis down the line.