USEARCH中文帮助文档(USEARCH Chinese manual)
USEARCH官方英文主页：http://www.drive5.com/usearch/
本站经USEARCH作者Robert Edgar授权，由《宏基因组》公众号翻译的中文帮助文档和系列教程。
所有软件版本的下载链接：https://github.com/rcedgar/usearch_old_binaries/，备用下载链接见"软件下载"
USEARCH是最好用的扩增子分析流程，在体积仅1 MB的软件中实现了近200种扩增子分析常用功能，安装方便且运行速度快。截止24年8月1日，Google学术统计引用20960次。
USEARCH作者是Robert Edgar独立研究员(Independent Investigator)在本领域开发了一系列经典算法和软件，如扩增子分析流程USEARCH[1]、嵌合体检测软件UCHIME[2]、OTU聚类和代表性序列鉴定算法UPARSE[3]、和测序数据错误过滤和校正的去噪算法UNOISE[4]等。这些新算法和软件的推出，极大的提高了扩增子数据分析的速度和准确度。USEARCH不仅分析速度快，而且软件可用性强，可有效降低入门学习成本并节约宝贵时间。
进一步阅读，欢迎点击下方链接，阅读宏基因组公众号关于USEARCH的历史文章。
- 体积小巧：QIIME系统软件大小上G，而USEARCH只有1M的大小完成了市面上的大多数分析功能；
- 安装方便：软件无依赖关系，下载后添加环境变量即可运行；
- 运行速度快：R语言在大数据面前太低效，USEARCH采用C编写，数据处理速度为R的20倍。鉴定ASV的核心算法UNOISE3也比主流软件DADA2[5]快100倍，delbur快10倍以上[6]，详见 主流非聚类方法dada2,deblur和unoise3介绍与比较；
- 跨平台：绝大多数软件只能在Linux上运行。USEARCH支持三大主流操作系统，不仅在Linux服务上跑的溜，而且在你的Windows/Mac笔记本上也可以轻松分析多达上千个样本的扩增子大数据。
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- Edgar RC: Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461.
- Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R: UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194-2200.
- Edgar RC: UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 2013, 10:996.
- Edgar RC, Flyvbjerg H: Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics 2015, 31:3476-3482.
- Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP: DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 2016, 13:581.
- Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech Xu Z, Kightley EP, Thompson LR, Hyde ER, Gonzalez A, et al.: Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2017, 2:e00191-00116.