Cloud Based Short Read Mapping Service

Abstract

Bioinformatics is an emerging field with seemingly limitless possibilities for advances in numerous scientific research and applications domains. In this paper, we summaries the explosive cutting-edge acceleration engines for the emerging short read mapping problems. What's more, we propose a novel Cloud based web service solution to the short read mapping problem in DNA sequencing, which greatly accelerates the task of aligning continuous incoming short length reads to uncertain known reference genomes. This approach is based on the pre-process of the reference genomes and iterative MapReduce jobs for aligning the continuous incoming reads. The MapReduce-based read-mapping algorithm is modeled after RMAP. Preliminary experimental results on incorporated MapReduce programming framework demonstrate that our proposed architecture and methods efficiently reduces the waiting time for large scale short reads applications. This architecture would be much important and efficient in future commercial personal gnome sequencing service.