My project is mapping of DNA to reference genome (hg19). I would be working in java and would be running on Hadoop. I am stuck at selection of algorithms for mapping to reference genome. I came across various algorithms for mapping but can't figure out which would suit the purpose of mapping better. Can anyone suggest an algorithm for mapping which can be scaled for large Data in relatively short time (MIT or GPL licensed is fine).
I am new to this field. Please correct me if I am wrong and would really appreciate any suggestion or correction.