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Resolving Load Balancing Issues in BWA on NUMA Multicore Architectures [chapter]

Charlotte Herzeel, Thomas J. Ashby, Pascal Costanza, Wolfgang De Meuter
2014 Lecture Notes in Computer Science  
Running BWA in multithreaded mode on a multi-socket server results in poor scaling behaviour.  ...  Additional load imbalance is also caused by the BWA code not anticipating certain hardware characteristics of multi-socket multicores, such as the non-uniform memory access time of the different cores.  ...  This work is funded by Intel, Janssen Pharmaceutica and by the Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT).  ... 
doi:10.1007/978-3-642-55195-6_21 fatcat:oinok3gqn5gllavaxrmujz4pnu

Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design [article]

Damla Senol Cali
2021 arXiv   pre-print
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics.  ...  First, we comprehensively analyze the tools in the genome assembly pipeline for long reads in multiple dimensions, uncovering bottlenecks and tradeoffs that different combinations of tools and different  ...  ., specialized accelerators, in-memory processing engines, and SIMD architecture) to resolve the bottlenecks.  ... 
arXiv:2111.01916v1 fatcat:lbwk74jcbjgqzeqk7gnb77asja