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QuRe：用于从下一代测序数据中重建病毒准种的软件。

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data.

机构信息

Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610-3633, USA.

出版信息

Bioinformatics. 2012 Jan 1;28(1):132-3. doi: 10.1093/bioinformatics/btr627. Epub 2011 Nov 15.

DOI:10.1093/bioinformatics/btr627
PMID:22088846
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3244773/
Abstract

SUMMARY

Next-generation sequencing (NGS) is an ideal framework for the characterization of highly variable pathogens, with a deep resolution able to capture minority variants. However, the reconstruction of all variants of a viral population infecting a host is a challenging task for genome regions larger than the average NGS read length. QuRe is a program for viral quasispecies reconstruction, specifically developed to analyze long read (>100 bp) NGS data. The software performs alignments of sequence fragments against a reference genome, finds an optimal division of the genome into sliding windows based on coverage and diversity and attempts to reconstruct all the individual sequences of the viral quasispecies--along with their prevalence--using a heuristic algorithm, which matches multinomial distributions of distinct viral variants overlapping across the genome division. QuRe comes with a built-in Poisson error correction method and a post-reconstruction probabilistic clustering, both parameterized on given error rates in homopolymeric and non-homopolymeric regions.

AVAILABILITY

QuRe is platform-independent, multi-threaded software implemented in Java. It is distributed under the GNU General Public License, available at https://sourceforge.net/projects/qure/.

CONTACT

ahnven@yahoo.it; ahnven@gmail.com

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

摘要

下一代测序（NGS）是一种用于高度变异病原体特征描述的理想框架，具有能够捕获少数变体的深度分辨率。然而，对于大于平均 NGS 读取长度的基因组区域，重建感染宿主的病毒群体的所有变体是一项具有挑战性的任务。QuRe 是一种用于病毒准种重建的程序，专门用于分析长读 (>100 bp) NGS 数据。该软件对序列片段与参考基因组进行比对，根据覆盖度和多样性找到将基因组最佳划分成滑动窗口的方法，并尝试使用启发式算法重建病毒准种的所有个体序列及其流行度，该算法通过匹配基因组划分中重叠的不同病毒变体的多项分布来实现。QuRe 带有内置的泊松错误校正方法和重建后的概率聚类，两者都针对给定的同源和非同源区域的错误率进行参数化。

可用性

QuRe 是一个独立于平台的、多线程的 Java 实现软件。它根据 GNU 通用公共许可证分发，可在 https://sourceforge.net/projects/qure/ 上获得。

联系方式

ahnven@yahoo.it; ahnven@gmail.com

补充信息

补充数据可在 Bioinformatics 在线获得。

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2
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BMC Bioinformatics. 2011;12 Suppl 6(Suppl 6):S1. doi: 10.1186/1471-2105-12-S6-S1. Epub 2011 Jul 28.
3
Sequencing technologies and genome sequencing.测序技术和基因组测序。
J Appl Genet. 2011 Nov;52(4):413-35. doi: 10.1007/s13353-011-0057-x. Epub 2011 Jun 23.
4
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