read length versus unique alignment rate

Question

[igor]

How does the read sequence length affect alignment rates? It's almost impossible to have 10 bp align uniquely, but 100 bp works fairly well. I was hoping to find some table or chart that may answer this question more definitively, but haven't been able to do so on my own.

I am mostly concerned in the context of read trimming and setting the minimum read length for mammalian genomes, but any info would be helpful.

[John]

Maybe make a graph like this: A: How to find the shortest k-mer length that is unique in a large genome

Answer 1

[GenoMax]

These two papers should be of interest:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226227/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927684/