• 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

ShōRAH：基于下一代测序数据估计混合样本的遗传多样性。

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.

机构信息

Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland.

出版信息

BMC Bioinformatics. 2011 Apr 26;12:119. doi: 10.1186/1471-2105-12-119.

DOI:10.1186/1471-2105-12-119
PMID:21521499
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3113935/
Abstract

BACKGROUND

With next-generation sequencing technologies, experiments that were considered prohibitive only a few years ago are now possible. However, while these technologies have the ability to produce enormous volumes of data, the sequence reads are prone to error. This poses fundamental hurdles when genetic diversity is investigated.

RESULTS

We developed ShoRAH, a computational method for quantifying genetic diversity in a mixed sample and for identifying the individual clones in the population, while accounting for sequencing errors. The software was run on simulated data and on real data obtained in wet lab experiments to assess its reliability.

CONCLUSIONS

ShoRAH is implemented in C++, Python, and Perl and has been tested under Linux and Mac OS X. Source code is available under the GNU General Public License at http://www.cbg.ethz.ch/software/shorah.

摘要

背景

随着下一代测序技术的发展，几年前被认为是不可行的实验现在已经成为可能。然而，尽管这些技术能够产生大量的数据，但序列读取容易出错。当研究遗传多样性时，这就构成了根本性的障碍。

结果

我们开发了 ShoRAH，这是一种用于量化混合样本中遗传多样性并识别群体中个体克隆的计算方法，同时考虑到测序错误。该软件在模拟数据和在湿实验室实验中获得的真实数据上运行，以评估其可靠性。

结论

ShoRAH 是用 C++、Python 和 Perl 编写的，并在 Linux 和 Mac OS X 下进行了测试。源代码可在 http://www.cbg.ethz.ch/software/shorah 下根据 GNU 通用公共许可证获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0585/3113935/1226c383c95c/1471-2105-12-119-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0585/3113935/9698c7423325/1471-2105-12-119-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0585/3113935/1226c383c95c/1471-2105-12-119-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0585/3113935/9698c7423325/1471-2105-12-119-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0585/3113935/1226c383c95c/1471-2105-12-119-2.jpg

相似文献

1
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.ShōRAH：基于下一代测序数据估计混合样本的遗传多样性。
BMC Bioinformatics. 2011 Apr 26;12:119. doi: 10.1186/1471-2105-12-119.
2
Inferring viral quasispecies spectra from 454 pyrosequencing reads.从 454 焦磷酸测序读取中推断病毒准种谱。
BMC Bioinformatics. 2011;12 Suppl 6(Suppl 6):S1. doi: 10.1186/1471-2105-12-S6-S1. Epub 2011 Jul 28.
3
Evaluation of haplotype callers for next-generation sequencing of viruses.病毒下一代测序中单体型caller 的评估。
Infect Genet Evol. 2020 Aug;82:104277. doi: 10.1016/j.meegid.2020.104277. Epub 2020 Mar 6.
4
NanoPack: visualizing and processing long-read sequencing data.NanoPack：可视化和处理长读测序数据。
Bioinformatics. 2018 Aug 1;34(15):2666-2669. doi: 10.1093/bioinformatics/bty149.
5
PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data.PAPNC，一种从大规模下一代测序数据计算核苷酸多样性的新方法。
J Virol Methods. 2014 Jul;203:73-80. doi: 10.1016/j.jviromet.2014.03.008. Epub 2014 Mar 26.
6
NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets.NGSUtils：一套用于分析和操作下一代测序数据集的软件套件。
Bioinformatics. 2013 Feb 15;29(4):494-6. doi: 10.1093/bioinformatics/bts731. Epub 2013 Jan 12.
7
ploidyNGS: visually exploring ploidy with Next Generation Sequencing data.ploidyNGS：使用下一代测序数据进行直观的倍性分析。
Bioinformatics. 2017 Aug 15;33(16):2575-2576. doi: 10.1093/bioinformatics/btx204.
8
Nautilus: a bioinformatics package for the analysis of HIV type 1 targeted deep sequencing data.鹦鹉螺：一个用于分析1型人类免疫缺陷病毒靶向深度测序数据的生物信息学软件包。
AIDS Res Hum Retroviruses. 2013 Oct;29(10):1361-4. doi: 10.1089/AID.2013.0175. Epub 2013 Aug 2.
9
A comprehensive quality control workflow for paired tumor-normal NGS experiments.用于配对肿瘤-正常样本二代测序（NGS）实验的全面质量控制工作流程。
Bioinformatics. 2017 Jun 1;33(11):1721-1722. doi: 10.1093/bioinformatics/btx032.
10
NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis.NGS-pipe：一个灵活、易于扩展且高度可配置的 NGS 分析框架。
Bioinformatics. 2018 Jan 1;34(1):107-108. doi: 10.1093/bioinformatics/btx540.

引用本文的文献

1
Temporal dynamics of viral fitness and the adaptive immune response in HCV infection.丙型肝炎病毒感染中病毒适应性和适应性免疫反应的时间动态变化
Elife. 2025 Aug 29;13:RP102232. doi: 10.7554/eLife.102232.
2
The Emerging Role of Omics-Based Approaches in Plant Virology.基于组学方法在植物病毒学中的新兴作用。
Viruses. 2025 Jul 15;17(7):986. doi: 10.3390/v17070986.
3
VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data.VILOCA：用于短读长和长读长数据的测序质量感知病毒单倍型重建及突变检测

本文引用的文献

1
HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model.使用传播狄利克雷过程混合模型进行HIV单倍型推断
IEEE/ACM Trans Comput Biol Bioinform. 2014 Jan-Feb;11(1):182-91. doi: 10.1109/TCBB.2013.145.
2
Genovo: de novo assembly for metagenomes.Genovo：宏基因组的从头组装
J Comput Biol. 2011 Mar;18(3):429-43. doi: 10.1089/cmb.2010.0244.
3
Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing.基于下一代测序的准种重建的组合分析和算法。
NAR Genom Bioinform. 2024 Nov 28;6(4):lqae152. doi: 10.1093/nargab/lqae152. eCollection 2024 Dec.
4
V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.V-pipe 3.0：一种用于样本内病毒遗传多样性估计的可持续性管道。
Gigascience. 2024 Jan 2;13. doi: 10.1093/gigascience/giae065.
5
Evolutionary Dynamics of Accelerated Antiviral Resistance Development in Hypermutator Herpesvirus.加速抗病毒耐药性发展的高突变率疱疹病毒的进化动态。
Mol Biol Evol. 2024 Jul 3;41(7). doi: 10.1093/molbev/msae119.
6
Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.追踪废水中的 SARS-CoV-2 关切变异株：使用模拟基因组数据评估九种计算工具。
Microb Genom. 2024 May;10(5). doi: 10.1099/mgen.0.001249.
7
Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation.联合宿主-病原体基因组分析鉴定与人类 NTCP 和 HLA Ⅰ类变异相关的乙型肝炎病毒突变。
Am J Hum Genet. 2024 Jun 6;111(6):1018-1034. doi: 10.1016/j.ajhg.2024.04.013. Epub 2024 May 14.
8
Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover.探索 SARS-CoV-2 基因组的低频等位基因变体表明，墨西哥的合并感染发生在 VOCs 更替期间。
Microb Genom. 2024 Mar;10(3). doi: 10.1099/mgen.0.001220.
9
All together now: Geographically coordinated miticide treatment benefits honey bee health.现在大家齐心协力：地理协调的杀螨剂处理有益于蜜蜂健康。
J Appl Ecol. 2023 May;60(5):790-802. doi: 10.1111/1365-2664.14367. Epub 2023 Jan 26.
10
Parallel evolution and enhanced virulence upon passage of an RNA virus in .一种RNA病毒传代后的平行进化与毒力增强
Virus Evol. 2023 Dec 15;9(2):vead074. doi: 10.1093/ve/vead074. eCollection 2023.
BMC Bioinformatics. 2011 Jan 5;12:5. doi: 10.1186/1471-2105-12-5.
4
Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies.下一代测序数据纠错和 HIV 准种可靠估计。
Nucleic Acids Res. 2010 Nov;38(21):7400-9. doi: 10.1093/nar/gkq655. Epub 2010 Jul 29.
5
Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction.基因异质样本的深度测序：局部单倍型重建与读段错误校正
J Comput Biol. 2010 Mar;17(3):417-28. doi: 10.1089/cmb.2009.0164.
6
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.在单核苷酸分辨率下分析的小叶型乳腺肿瘤中的突变进化。
Nature. 2009 Oct 8;461(7265):809-13. doi: 10.1038/nature08489.
7
Genome-wide mutational diversity in an evolving population of Escherichia coli.大肠杆菌进化群体中的全基因组突变多样性
Cold Spring Harb Symp Quant Biol. 2009;74:119-29. doi: 10.1101/sqb.2009.74.018. Epub 2009 Sep 23.
8
Viral population estimation using pyrosequencing.使用焦磷酸测序法进行病毒群体估计。
PLoS Comput Biol. 2008 May 9;4(4):e1000074. doi: 10.1371/journal.pcbi.1000074.
9
Population sequencing using short reads: HIV as a case study.使用短读长的群体测序：以HIV为例的案例研究。
Pac Symp Biocomput. 2008:114-25.
10
Evolutionary and immunological implications of contemporary HIV-1 variation.当代HIV-1变异的进化和免疫学意义
Br Med Bull. 2001;58:19-42. doi: 10.1093/bmb/58.1.19.