nf-UnO流程：一种用于从宏基因组下一代测序疫情数据集检测新型病原体的宏基因组共组装流程。
nf-UnO pipeline: A metagenomic co-assembly pipeline for novel pathogen detection from mNGS outbreak sets.
作者信息
Guzman-Cole Candace, Huang Andrew D
机构信息
Enteric Diseases Laboratory Branch, Centers for Disease Control, Atlanta, GA 30322, United States.
出版信息
Bioinformatics. 2025 Aug 2;41(8). doi: 10.1093/bioinformatics/btaf436.
Abstract
SUMMARY
nf-UnO is a pipeline implemented in Nextflow to identify novel pathogens from metagenomic shotgun sequencing of epidemiologically related foodborne outbreak specimens. nf-UnO uses MIDAS2, metagenomic co-assembly, multiple binning programs, and read mapping to metagenomically assembled genomes to detect potential etiological agents found in common across outbreak specimens.
AVAILABILITY AND IMPLEMENTATION
摘要
摘要
nf-UnO是一个用Nextflow实现的流程，用于从与流行病学相关的食源性暴发样本的宏基因组鸟枪法测序中识别新型病原体。nf-UnO使用MIDAS2、宏基因组共组装、多个分箱程序以及将 reads 映射到宏基因组组装基因组上，以检测在暴发样本中共同发现的潜在病原体。
可用性和实现方式
相似文献
1
nf-UnO pipeline: A metagenomic co-assembly pipeline for novel pathogen detection from mNGS outbreak sets.nf-UnO流程：一种用于从宏基因组下一代测序疫情数据集检测新型病原体的宏基因组共组装流程。
Bioinformatics. 2025 Aug 2;41(8). doi: 10.1093/bioinformatics/btaf436.
2
Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2.经验教训：通过CoVpipe2从短读长测序数据重建严重急性呼吸综合征冠状病毒2（SARS-CoV-2）基因组时克服常见挑战。
F1000Res. 2024 Apr 16;12:1091. doi: 10.12688/f1000research.136683.1. eCollection 2023.
3
Clinical value of metagenomic next-generation sequencing in patients with connective tissue diseases co-infections: a single-center study from southern hospital in China.宏基因组二代测序在结缔组织病合并感染患者中的临床价值：来自中国南方医院的单中心研究
Clin Rheumatol. 2025 Jun 20. doi: 10.1007/s10067-025-07525-6.
4
An open-source nanopore-only sequencing workflow for analysis of clonal outbreaks delivers short-read level accuracy.一种用于分析克隆性暴发的仅基于纳米孔的开源测序工作流程可实现短读长水平的准确性。
J Clin Microbiol. 2025 Jul 18:e0066425. doi: 10.1128/jcm.00664-25.
5
Deploying Metagenomics to Characterize Microbial Pathogens During Outbreak of Acute Febrile Illness Among Children in Tanzania.利用宏基因组学对坦桑尼亚儿童急性发热性疾病暴发期间的微生物病原体进行特征分析。
Pathogens. 2025 Jun 19;14(6):601. doi: 10.3390/pathogens14060601.
6
HIVGenoPipe: a nextflow pipeline for the detection of HIV-1 drug resistance using a real-time sample-specific reference sequence.HIVGenoPipe：一种用于使用实时样本特异性参考序列检测HIV-1耐药性的Nextflow管道。
BMC Bioinformatics. 2025 Jul 7;26(1):168. doi: 10.1186/s12859-025-06201-5.
7
Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Central Nervous System Infections: Advances and Challenges.临床宏基因组下一代测序在中枢神经系统感染诊断中的应用：进展与挑战。
Mol Diagn Ther. 2024 Sep;28(5):513-523. doi: 10.1007/s40291-024-00727-9. Epub 2024 Jul 11.
8
Comparison of microbial culture, metagenomic next-generation sequencing and droplet digital polymerase chain reaction methods for pathogen detection in patients with neurosurgical central nervous system infection.微生物培养、宏基因组新一代测序和液滴数字聚合酶链反应方法在神经外科中枢神经系统感染患者病原体检测中的比较
Front Cell Infect Microbiol. 2025 Jul 30;15:1606283. doi: 10.3389/fcimb.2025.1606283. eCollection 2025.
9
METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses.METAnnotatorX2：用于深度和浅层宏基因组数据集分析的综合工具。
mSystems. 2021 Jun 29;6(3):e0058321. doi: 10.1128/mSystems.00583-21.
10
Mapler: a pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads.Mapler：一种用于评估使用高保真读段测序的分类丰富宏基因组中组装质量的流程。
Bioinformatics. 2025 Jun 2;41(6). doi: 10.1093/bioinformatics/btaf334.
本文引用的文献
1
Clinical metagenomics-challenges and future prospects.临床宏基因组学——挑战与未来前景
Front Microbiol. 2023 Jun 28;14:1186424. doi: 10.3389/fmicb.2023.1186424. eCollection 2023.
2
MIDAS2: Metagenomic Intra-species Diversity Analysis System.MIDAS2：种内宏基因组多样性分析系统。
Bioinformatics. 2023 Jan 1;39(1). doi: 10.1093/bioinformatics/btac713.
3
nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.nf-core/mag：宏基因组混合组装与分箱的最佳实践流程。
NAR Genom Bioinform. 2022 Feb 2;4(1):lqac007. doi: 10.1093/nargab/lqac007. eCollection 2022 Mar.
4
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy.GTDB：通过系统发生一致、等级归一化和基于完整基因组的分类学，对细菌和古菌多样性进行持续普查。
Nucleic Acids Res. 2022 Jan 7;50(D1):D785-D794. doi: 10.1093/nar/gkab776.
5
A unified catalog of 204,938 reference genomes from the human gut microbiome.人类肠道微生物组 204938 个参考基因组的统一目录。
Nat Biotechnol. 2021 Jan;39(1):105-114. doi: 10.1038/s41587-020-0603-3. Epub 2020 Jul 20.
6
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies.MetaBAT 2：一种用于从宏基因组组装中进行稳健且高效的基因组重建的自适应分箱算法。
PeerJ. 2019 Jul 26;7:e7359. doi: 10.7717/peerj.7359. eCollection 2019.
7
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.高通量 ANI 分析 9 万余组原核基因组揭示了清晰的物种界限。
Nat Commun. 2018 Nov 30;9(1):5114. doi: 10.1038/s41467-018-07641-9.
8
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.通过去重、聚合和评分策略从宏基因组中恢复基因组。
Nat Microbiol. 2018 Jul;3(7):836-843. doi: 10.1038/s41564-018-0171-1. Epub 2018 May 28.
9
Nextflow enables reproducible computational workflows.Nextflow支持可重复的计算工作流程。
Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820.
10
Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods.两起严重食源性疾病暴发的宏基因组学研究揭示了传统方法无法获得的诊断特征和共感染迹象。
Appl Environ Microbiol. 2017 Jan 17;83(3). doi: 10.1128/AEM.02577-16. Print 2017 Feb 1.
Zotero 插件