Sequence alignment is a widely-used tool in genomics. With the development of next generation sequencing (NGS) technology, the production of sequence read data has recently increased. A number of read alignment algorithms for handling NGS data have been developed. However, these algorithms suffer from a trade-off between the throughput and alignment quality, due to the large computational costs for processing repeat reads. Conversely, alignment algorithms with distributed systems such as Hadoop and Trinity can obtain a better throughput than existing algorithms on single machine without compromising the alignment quality. In this paper, we suggest BulkAligner, a novel sequence alignment algorithm on the graph-based in-memory distributed system Trinity. We covert the original reference sequence into graph form and perform sequence alignment by finding the longest paths on the graph. Our experimental results show that BulkAligner has at least an 1.8× and up to 57× better throughput with the same, or higher quality than existing algorithms with Hadoop. We analyze the scalability and show that we can obtain a better throughput by simply adding machines.
Bibliographical noteFunding Information:
I would like to thank Bin Shao, Haixun Wang for introducing me to Trinity. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP) ( 2012R1A2A1A01010775 ). Sanghyun Park is corresponding author of this paper.
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All Science Journal Classification (ASJC) codes
- Control and Systems Engineering
- Theoretical Computer Science
- Computer Science Applications
- Information Systems and Management
- Artificial Intelligence