Efficient genomic read alignment in an in-memory database

摘要

The present application refers to high performance, low-cost, gapped read alignment that produces high quality alignments of a complete human genome in a few minutes. Additionally the algorithm is more than an order of magnitude faster than previous approaches using a low-cost workstation. The result is obtained via careful algorithm engineering of the seeding based approach. The use of non-hashed seeds and combine them using techniques from search engine ranking to achieve fast cache-efficient processing. The algorithm can also be well parallelized. Integration into an in-memory database infrastructure (IMDB) leads to low overhead for data management and further analysis.