SquiggleFilter: An accelerator for portable virus detection

Abstract

The MinION is a recent-to-market handheld nanopore sequencer. It can be used to determine the whole genome of a target virus in a biological sample. Its Read Until feature allows us to skip sequencing a majority of non-target reads (DNA/RNA fragments), which constitutes more than 99% of all reads in a typical sample. However, it does not have any on-board computing, which significantly limits its portability. We analyze the performance of a Read Until metagenomic pipeline for detecting target viruses and identifying strain-specific mutations. We find new sources of performance bottlenecks (basecaller in classification of a read) that are not addressed by past genomics accelerators. We present SquiggleFilter, a novel hardware accelerated dynamic time warping (DTW) based filter that directly analyzes Min- ION's raw squiggles and filters everything except target viral reads, thereby avoiding the expensive basecalling step. We show that our 14.3W 13.25mm2 accelerator has 274× greater throughput and 3481× lower latency than existing GPU-based solutions while consuming half the power, enabling Read Until for the next generation of nanopore sequencers.