Optimizing Burrows-Wheeler Transform-Based Sequence Alignment on Multicore Architectures

Jing Zhang, Heshan Lin, Pavan Balaji, Wu-Chun Feng
2013 2013 13th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing  
Computational biology sequence alignment tools using the Burrows-Wheeler Transform (BWT) are widely used in next-generation sequencing (NGS) analysis. However, despite extensive optimization efforts, the performance of these tools still cannot keep up with the explosive growth of sequencing data. Through an in-depth performance analysis of BWA, a popular BWT-based aligner on multicore architectures, we demonstrate that such tools are limited by memory bandwidth due to their irregular memory
more » ... ss patterns. We then propose a locality-aware implementation of BWA that aims at optimizing its performance by better exploiting the caching mechanisms of modern multicore processors. Experimental results show that our improved BWA implementation can reduce last-level cache (LLC) misses by 30% and translation lookaside buffer (TLB) misses by 20%, resulting in up to 2.6fold speedup over the original BWA implementation.
doi:10.1109/ccgrid.2013.67 dblp:conf/ccgrid/ZhangLBF13 fatcat:6olzfr37wfcjvp62vboodprqfa