Noc-Enabled Software/Hardware Co-Design Framework For Accelerating K-Mer Counting

Counting k-mers (substrings of fixed length k) in DNA and protein sequences generate non-uniform and irregular memory access patterns. Processing-in-Memory (PIM) architectures have the potential to significantly reduce the overheads associated with such frequent and irregular memory accesses. However, existing k-mer counting algorithms are not designed to exploit the advantages of PIM architectures. Furthermore, owing to thermal constraints, the allowable power budget is limited in conventional PIM designs. Moreover, k-mer counting generates unbalanced and long-range traffic patterns that need to be handled by an efficient Network-on-Chip (NoC). In this paper, we present an NoC-enabled software/hardware co-design framework to implement high-performance k-mer counting. The proposed architecture enables more computational power, efficient communication between cores/memory - all without creating a thermal bottleneck; while the software component exposes more in-memory opportunities to exploit the PIM and aids in the NoC design. Experimental results show that the proposed architecture outperforms a state-of-the-art software implementation of k-mer counting utilizing Hybrid Memory Cube (HMC), by up to 7.14X, while allowing significantly higher power budgets.