Supporting data for "iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone"

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 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 of viral and bacterial genomes 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 in GitHub and for free on Apple’s App Store.过去数十年来，随着集成电路与其他计算机硬件不断微型化，DNA测序技术也正遵循着相似的发展路径。引领这一趋势的是牛津纳米孔测序平台（Oxford Nanopore sequencing platform），其目前已推出手持式MinION测序仪，且更小型的测序设备已在研发进程中。该技术已应用于多项重要场景，其中包括全球偏远站点的重大病原体基因组分析工作。然而，尽管该测序仪操作简便，但与之匹配的简易便携分析平台仍暂未问世。iGenomics是首款综合性移动基因组分析应用，可在iOS设备上独立完成读段比对、变异检出与结果可视化全流程操作。该应用采用Objective-C语言开发，基于FM索引（FM-index）、带状动态规划（banded dynamic programming）等高性能生物信息学技术，针对移动设备运行环境进行了专项优化。我们通过多套真实与模拟的病毒、细菌基因组纳米孔测序数据集对iGenomics开展性能基准测试，结果显示其性能可媲美主流的BWA-MEM/Samtools/IGV工具套件，且无需依赖笔记本电脑或服务器集群。iGenomics已在GitHub平台开源，并可在苹果应用商店免费获取。