• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

从长的未校正读段中进行快速且准确的从头基因组组装。

Fast and accurate de novo genome assembly from long uncorrected reads.

作者信息

Vaser Robert, Sović Ivan, Nagarajan Niranjan, Šikić Mile

机构信息

Department of Electronic Systems and Information Processing, University of Zagreb, Faculty of Electrical Engineering and Computing, 10000 Zagreb, Croatia.

Centre for Informatics and Computing, Ruđer Bošković Institute, 10000 Zagreb, Croatia.

出版信息

Genome Res. 2017 May;27(5):737-746. doi: 10.1101/gr.214270.116. Epub 2017 Jan 18.

DOI:10.1101/gr.214270.116
PMID:28100585
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5411768/
Abstract

The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource-intensive error-correction and consensus-generation steps to obtain high-quality assemblies. We show that the error-correction step can be omitted and that high-quality consensus sequences can be generated efficiently with a SIMD-accelerated, partial-order alignment-based, stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore data sets, we show that Racon coupled with miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster.

摘要

来自太平洋生物科学公司（Pacific Biosciences）和牛津纳米孔技术公司（Oxford Nanopore Technologies）的长读长序列组装通常需要资源密集型的纠错和生成一致序列步骤，以获得高质量的组装结果。我们表明，可以省略纠错步骤，并且使用一个名为Racon的基于单指令多数据（SIMD）加速、基于偏序比对的独立一致序列模块，能够高效地生成高质量的一致序列。基于对PacBio和牛津纳米孔数据集的测试，我们表明，Racon与miniasm相结合，能够生成质量与现有最先进方法相似或更好的一致基因组，同时速度快一个数量级。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/3cd82af9930a/737a03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/a3dcc56780ef/737f01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/e542eceb3e1c/737f02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/1e66a23b4ca9/737f03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/e96344c52427/737a01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/ed604b9e6f5f/737a02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/412c7b7c3bb9/737f04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/3cd82af9930a/737a03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/a3dcc56780ef/737f01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/e542eceb3e1c/737f02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/1e66a23b4ca9/737f03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/e96344c52427/737a01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/ed604b9e6f5f/737a02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/412c7b7c3bb9/737f04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4692/5411768/3cd82af9930a/737a03.jpg

相似文献

1
Fast and accurate de novo genome assembly from long uncorrected reads.从长的未校正读段中进行快速且准确的从头基因组组装。
Genome Res. 2017 May;27(5):737-746. doi: 10.1101/gr.214270.116. Epub 2017 Jan 18.
2
Canu: scalable and accurate long-read assembly via adaptive -mer weighting and repeat separation.Canu：通过自适应k-mer加权和重复序列分离实现可扩展且准确的长读长序列拼接
Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15.
3
Benchmarking Long-Read Assemblers for Genomic Analyses of Bacterial Pathogens Using Oxford Nanopore Sequencing.基于 Oxford Nanopore 测序的细菌病原体基因组分析的长读长组装器基准测试
Int J Mol Sci. 2020 Dec 1;21(23):9161. doi: 10.3390/ijms21239161.
4
Improved assembly of noisy long reads by k-mer validation.通过k-mer验证改进嘈杂长读段的组装。
Genome Res. 2016 Dec;26(12):1710-1720. doi: 10.1101/gr.209247.116. Epub 2016 Oct 7.
5
Hybrid assembly of the large and highly repetitive genome of , a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.利用MaSuRCA巨读算法对面包小麦的祖先之一——[具体物种名称未给出]的大型高度重复基因组进行混合组装。
Genome Res. 2017 May;27(5):787-792. doi: 10.1101/gr.213405.116. Epub 2017 Jan 27.
6
Highly accurate long reads are crucial for realizing the potential of biodiversity genomics.高质量的长读长序列对于实现生物多样性基因组学的潜力至关重要。
BMC Genomics. 2023 Mar 16;24(1):117. doi: 10.1186/s12864-023-09193-9.
7
Benchmarking of de novo assembly algorithms for Nanopore data reveals optimal performance of OLC approaches.用于纳米孔数据的从头组装算法基准测试揭示了重叠布局一致（OLC）方法的最佳性能。
BMC Genomics. 2016 Aug 22;17 Suppl 7(Suppl 7):507. doi: 10.1186/s12864-016-2895-8.
8
Direct comparison of performance of single nucleotide variant calling in human genome with alignment-based and assembly-based approaches.直接比较基于比对和组装的方法在人类基因组中单核苷酸变异calling 的性能。
Sci Rep. 2017 Sep 8;7(1):10963. doi: 10.1038/s41598-017-10826-9.
9
HINGE: long-read assembly achieves optimal repeat resolution.HINGE：长读长组装可实现最佳的重复序列解析。
Genome Res. 2017 May;27(5):747-756. doi: 10.1101/gr.216465.116. Epub 2017 Mar 20.
10
Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing.使用 Illumina 和 Oxford Nanopore 测序对细菌病原体进行基因组分析的混合组装方法的基准测试。
BMC Genomics. 2020 Sep 14;21(1):631. doi: 10.1186/s12864-020-07041-8.

引用本文的文献

1
One mother for two species via obligate cross-species cloning in ants.蚂蚁通过专性跨物种克隆实现两个物种共享一位蚁后。
Nature. 2025 Sep 3. doi: 10.1038/s41586-025-09425-w.
2
Chromosome-level assembly of cv. 'Tokiwa' as a reference genome of Japanese cucumber.栽培品种‘常盘’的染色体水平组装，作为日本黄瓜的参考基因组。
Breed Sci. 2025 Apr;75(2):85-92. doi: 10.1270/jsbbs.24066. Epub 2025 Mar 27.
3
Genomic and Phenotypic Evaluation of the Gliadin-Degrading Probiotic Bacillus amyloliquefaciens EG025 from Cheonggukjang for Celiac Disease Treatment.

本文引用的文献

1
Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.Edlib：一个使用编辑距离进行快速、精确序列比对的C/C++库。
Bioinformatics. 2017 May 1;33(9):1394-1395. doi: 10.1093/bioinformatics/btw753.
2
de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer.使用牛津纳米孔MinION测序仪对天然酵母分离株进行从头组装和群体基因组调查。
Gigascience. 2017 Feb 1;6(2):1-13. doi: 10.1093/gigascience/giw018.
3
Canu: scalable and accurate long-read assembly via adaptive -mer weighting and repeat separation.
用于治疗乳糜泻的清国酱源解醇溶蛋白益生菌解淀粉芽孢杆菌EG025的基因组和表型评估
Probiotics Antimicrob Proteins. 2025 Sep 2. doi: 10.1007/s12602-025-10728-7.
4
A telomere-to-telomere genome assembly of koi carp (Cyprinus carpio) using long reads and Hi-C technology.利用长读长和Hi-C技术对锦鲤（Cyprinus carpio）进行端粒到端粒的基因组组装。
Gigascience. 2025 Jan 6;14. doi: 10.1093/gigascience/giaf087.
5
Accurately assembling nanopore sequencing data of highly pathogenic bacteria.准确组装高致病性细菌的纳米孔测序数据。
BMC Genomics. 2025 Aug 28;26(1):783. doi: 10.1186/s12864-025-11793-6.
6
Highly contiguous genome of the medicinal plant Sarcandra glabra (Thunb.) Nakai.药用植物九节龙（学名：Sarcandra glabra (Thunb.) Nakai）的高度连续基因组。
Sci Data. 2025 Aug 28;12(1):1508. doi: 10.1038/s41597-025-05796-x.
7
Re-annotation improved large-scale assembly of the reef-building coral Acropora intermedia.重新注释改进了造礁珊瑚中间鹿角珊瑚的大规模组装。
Sci Data. 2025 Aug 28;12(1):1504. doi: 10.1038/s41597-025-05849-1.
8
Genomic Insights into Emerging Multidrug-Resistant Strains: First Report from Thailand.对新兴多重耐药菌株的基因组学见解：来自泰国的首次报告。
Antibiotics (Basel). 2025 Jul 24;14(8):746. doi: 10.3390/antibiotics14080746.
9
Complex Sex Determination in the Grey Mullet Suggested by Individual Whole Genome Sequence Data.个体全基因组序列数据表明鲻鱼存在复杂的性别决定机制。
Animals (Basel). 2025 Aug 20;15(16):2445. doi: 10.3390/ani15162445.
10
The bacterial community of the freshwater bryozoan Cristatella Mucedo and its secondary metabolites production potential.淡水苔藓虫穆氏冠苔藓虫的细菌群落及其次生代谢产物的产生潜力。
Sci Rep. 2025 Aug 26;15(1):31456. doi: 10.1038/s41598-025-17084-0.
Canu：通过自适应k-mer加权和重复序列分离实现可扩展且准确的长读长序列拼接
Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116. Epub 2017 Mar 15.
4
Phased diploid genome assembly with single-molecule real-time sequencing.基于单分子实时测序的阶段性二倍体基因组组装
Nat Methods. 2016 Dec;13(12):1050-1054. doi: 10.1038/nmeth.4035. Epub 2016 Oct 17.
5
Real-time selective sequencing using nanopore technology.使用纳米孔技术的实时选择性测序。
Nat Methods. 2016 Sep;13(9):751-4. doi: 10.1038/nmeth.3930. Epub 2016 Jul 25.
6
Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads.Sparc：一种用于长错误测序读数的基于稀疏性的共识算法。
PeerJ. 2016 Jun 8;4:e2016. doi: 10.7717/peerj.2016. eCollection 2016.
7
Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads.用于纳米孔读数从头组装的混合与非混合方法评估
Bioinformatics. 2016 Sep 1;32(17):2582-9. doi: 10.1093/bioinformatics/btw237. Epub 2016 May 9.
8
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.Minimap和miniasm：用于有噪声长序列的快速映射和从头组装。
Bioinformatics. 2016 Jul 15;32(14):2103-10. doi: 10.1093/bioinformatics/btw152. Epub 2016 Mar 19.
9
Fast and sensitive mapping of nanopore sequencing reads with GraphMap.使用GraphMap对纳米孔测序读数进行快速灵敏的映射
Nat Commun. 2016 Apr 15;7:11307. doi: 10.1038/ncomms11307.
10
A complete bacterial genome assembled de novo using only nanopore sequencing data.仅使用纳米孔测序数据从头组装完整的细菌基因组。
Nat Methods. 2015 Aug;12(8):733-5. doi: 10.1038/nmeth.3444. Epub 2015 Jun 15.