  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.
