IGenomics: Comprehensive DNA sequence analysis on your Smartphone

Aspyn Palatnick, Bin Zhou, Elodie Ghedin, Michael C. Schatz

Research output: Contribution to journalArticlepeer-review

Abstract

Background. Following the miniaturization of integrated circuitry and other computer hardware over the past several decades, DNA sequencing is on 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 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. Results. 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 of viral and bacterial genomes and show that iGenomics has performance comparable to the popular BWA-MEM/SAMtools/IGV suite, without necessitating a laptop or server cluster. Conclusions. iGenomics is available open source (https://github.com/stuckinaboot/iGenomics) and for free on Apple's App Store (https://apple.co/2HCplzr).

Original languageEnglish (US)
Article numbergiaa138
JournalGigaScience
Volume9
Issue number12
DOIs
StatePublished - Dec 1 2021

Keywords

  • DNA sequencing
  • Mobile computing
  • Variant analysis

ASJC Scopus subject areas

  • Health Informatics
  • Computer Science Applications

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