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iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone

Aspyn Palatnick, Bin Zhou, Elodie Ghedin, View ORCID ProfileMichael C. Schatz
doi: https://doi.org/10.1101/2020.02.11.944132
Aspyn Palatnick
1Cold Spring Harbor High School, Cold Spring Harbor, NY 11724
2Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
3University of Pennsylvania, Philadelphia, PA 19104
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Bin Zhou
4Department of Biology, New York University, New York, NY 10003
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Elodie Ghedin
4Department of Biology, New York University, New York, NY 10003
5Department of Epidemiology, School of Global Public Health, New York, NY 10003
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Michael C. Schatz
2Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
6Departments of Computer Science and Biology, Johns Hopkins University, Baltimore MD, 21211
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  • ORCID record for Michael C. Schatz
  • For correspondence: mschatz@cshl.edu
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Abstract

Following the miniaturization of integrated circuitry and other computer hardware over the past several decades, DNA sequencing is following a similar path. Leading this trend is the Oxford Nanopore sequencing platform, which currently offers the hand-held MinION instrument and even smaller instruments on the near horizon. This technology has been used in several important applications, including the analysis of genomes of major pathogens in remote stations around the world. However, despite the simplicity of the sequencer, an equally simple and portable analysis platform is not yet available.

iGenomics is the first comprehensive mobile genome analysis application, with capabilities to align reads, call variants, and visualize the results entirely on an iOS device. Implemented in Objective-C using the FM-index, banded dynamic programming, and other high-performance bioinformatics techniques, iGenomics is optimized to run in a mobile environment. We benchmark iGenomics using a variety of real and simulated Nanopore sequencing datasets and show that iGenomics has performance comparable to the popular BWA-MEM/Samtools/IGV suite, without needing a laptop or server cluster. iGenomics is available open-source (https://github.com/stuckinaboot/iGenomics) and for free on Apple’s App Store (https://apps.apple.com/us/app/igenomics-mobile-dna-analysis/id1495719841).

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 12, 2020.
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iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone
Aspyn Palatnick, Bin Zhou, Elodie Ghedin, Michael C. Schatz
bioRxiv 2020.02.11.944132; doi: https://doi.org/10.1101/2020.02.11.944132
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iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone
Aspyn Palatnick, Bin Zhou, Elodie Ghedin, Michael C. Schatz
bioRxiv 2020.02.11.944132; doi: https://doi.org/10.1101/2020.02.11.944132

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