SquiggleFilter: An Accelerator for Portable Virus Detection

TL;DR

SquiggleFilter is a hardware accelerator that enables real-time, power-efficient virus detection on portable nanopore sequencers by directly analyzing raw signals and filtering non-target reads, significantly improving speed and efficiency.

Contribution

We introduce SquiggleFilter, a novel hardware accelerator for direct analysis of nanopore raw signals, enabling fast, low-power virus detection without basecalling.

Findings

Achieves 274X throughput improvement over GPUs

Reduces latency by 3481X compared to existing solutions

Consumes half the power of GPU-based methods

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 MinION'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 274X greater throughput and 3481X lower latency than existing GPU-based solutions while consuming half the power, enabling Read Until for the next generation of nanopore sequencers.