Data from: A MinION™‐based pipeline for fast and cost‐effective DNA barcoding

DNA barcodes are useful for species discovery and species identification, but obtaining barcodes currently requires a well-equipped molecular laboratory, is time-consuming, and/or expensive. We here address these issues by developing a barcoding pipeline for Oxford Nanopore MinION™ and demonstrate that one flowcell can generate barcodes for ~500 specimens despite high base-call error rates of MinION™ reads. The pipeline overcomes the errors by first summarizing all reads for the same tagged amplicon as a consensus barcode. Consensus barcodes are overall mismatch-free but retain indel errors that are concentrated in homopolymeric regions. They are addressed with an optional error correction pipeline that uses conserved amino-acid motifs from publicly available barcodes to correct the indel errors. The effectiveness of this pipeline is documented by analysing reads from three MinION™ runs that represent different stages of MinION™ development. They generated data for (1) 511 specimens of a mixed Diptera sample, (2) 575 specimens of ants, and (3) 50 specimens of Chironomidae. The run based on the latest chemistry yielded MinION barcodes for 490 of the 511 specimens which were assessed against reference Sanger barcodes (N=471). Overall, the MinION barcodes have an accuracy of 99.3%-100% and the number of post-correction ambiguities ranges from &lt;0.01-1.5% depending on which correction pipeline is used. We demonstrate that it requires ~2 hours of sequencing to gather all information needed for obtaining reliable barcodes for most specimens (&gt;90%). We estimate that up to 1000 barcodes can be generated in one flowcell and that the cost per barcode can beDNA条形码(DNA barcodes)在物种发现与物种鉴定中具备重要应用价值，但当前获取条形码仍需配备完善的分子生物学实验室，且耗时较长、成本高昂。本研究针对上述问题，开发了一套适配牛津纳米孔MinION™测序仪的条形码构建流程，并证实即便MinION™测序读段存在较高的碱基识别错误率，单张流动槽仍可完成约500份标本的条形码生成。该流程首先将同一标记扩增子的所有读段整合为共识条形码(consensus barcode)，以此校正测序错误。共识条形码整体无碱基错配，但仍存在集中于同源多聚区域(homopolymeric regions)的插入缺失错误(indel errors)；对此可通过可选的错误校正流程进行修复，该流程利用公共数据库中已公开条形码的保守氨基酸基序(conserved amino-acid motifs)来校正插入缺失错误。我们通过分析三次代表不同研发阶段的MinION™测序运行数据，验证了该流程的有效性：这三次测序分别为(1)混合双翅目(Diptera)样本的511份标本、(2)蚂蚁样本的575份标本、(3)摇蚊科(Chironomidae)样本的50份标本。基于最新测序化学试剂的测序运行中，511份待评估标本里有490份生成了MinION™条形码，并与471份桑格(Sanger)参考条形码进行了比对。整体而言，MinION™条形码的准确率可达99.3%~100%，且根据所选用的校正流程不同，校正后序列的歧义碱基占比范围为<0.01%~1.5%。研究证实，仅需约2小时的测序时长，即可获取大多数样本（>90%）的可靠条形码所需的全部信息。我们估算，单张流动槽最多可生成1000条条形码，且每条条形码的单条成本可

搜集汇总

背景与挑战

背景概述

该数据集支持一项基于Oxford Nanopore MinION™的快速、低成本DNA条形码管道研究，包含三个MinION™运行的数据，针对昆虫样本（如双翅目、蚂蚁和摇蚊），通过共识条形码和错误校正实现高准确性（达99.3%-100%），总数据量约3.33 GB，用于物种发现和鉴定。