SquiggleFilter: An Accelerator for Portable Virus Detection
Tim Dunn, Harisankar Sadasivan, Jack Wadden, Kush Goliya, Kuan-Yu Chen, David Blaauw, Reetuparna Das, Satish Narayanasamy
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.
Topics & Concepts
MinionSoftware portabilityComputer scienceNanopore sequencingDNA sequencerSample (material)DNA sequencingComputational biologyOperating systemDNABiologyGeneticsChromatographyChemistryBacteriophages and microbial interactionsGenomics and Phylogenetic StudiesPlant Virus Research Studies