SeGraM

SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping

PDF

code: C software implementation

Due to the nascent nature of sequence-to-graph mapping, a much smaller number of software tools (and no hardware accelerators) exist for sequence-to-graph mapping compared to the traditional sequence-to-sequence mapping.

Software tools analysis

we rigorously analyze two such tools, GraphAligner [61] and vg [36], running on an Intel Xeon E5-2630 v4 CPU [133] with 20 physical cores/40 logical cores with hyper-threading [134-137], operating at 2.20GHz, with 128GB DDR4 memory. Based on our bottleneck analysis with Intel VTune [138] and Linux Perf Tools [139], we make four key observations.

We use the cache-misses metric from Linux Perf Tools.

• Intel VTune: Intel Corp., “Intel® VTune™ Profiler.” Available
• Linux Perf Tools: WikiChip, “Perf: Linux Profiling with Performance Counters.” Available