SquiggleFilter: An Accelerator for Portable Virus Detection
Tim Dunn, Harisankar Sadasivan, Jack Wadden, Kush Goliya, Kuan-Yu, Chen, Reetuparna Das, David Blaauw, Satish Narayanasamy

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…
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Taxonomy
TopicsGenomics and Phylogenetic Studies · Algorithms and Data Compression · RNA and protein synthesis mechanisms
