QIIME 2：可重复、交互和扩展的微生物组数据分析流程
2010年发表于Nature Methods的QIIME[发音同chime]是微生物组领域最广泛使用的扩增子数据分析流程，截止2018年12月16日，Google Scholar统计引用13,126次。随着近年来测序通量的提高，大规模研究开展，其软件架构己法满足当前微生物组可重复分析的要求。
为满足当前大数据、可重复分析的需求，由QIIME第一作者Gregory Caporaso领衔于2016年从头开发的QIIME2，于2018年全面接档QIIME。文章正在投稿中，全文的预印版于10月24日发布于Peer J预印本，于本月3号更新了第二版，今天一起来了解一下关于QIIME2的最新消息吧！
QIIME2：可重复、可交互、适用范围广和可扩展的微生物组数据科学
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
PeerJ Preprints
DOI: https://doi.org/10.7287/peerj.preprints.27295v2
第一作者：Evan Bolyen1, Jai Ram Rideout1, Matthew R Dillon1, Nicholas A Bokulich1,
通讯作者：J Gregory Caporaso1,21 gregcaporaso@gmail.com
主要单位：美国，北亚利桑那大学，病原和微生物组研究所
本文共有112位作者，74家单位参与，除第一作者和通讯作者外，其他作者按姓氏字母顺序排列。作者和单位列表见附录。
摘要
我们推出了开源的微生物组数据科学平台——QIIME 2，适用于微生物生态领域研究人员的科学家、工程师，以及临床医生和决策者。QIIME 2的新特征将会推动微生物研究进入新的阶段。主要包括时间和空间分析和可视化工具，支持代谢组和宏基因组数据分析，自动化数据来源追溯确保数据的可重复，微生物组数据科学透明。
正文
图1. 交互式可视化工具
QIIME2提供了众多的交互式可视化工具。本图展示了4个示例，这些屏幕截图的交互版本详见 https://github.com/qiime2/paper1 (快访问体验一下吧)。这些图绘制的详细代码、描述详见在线方法部分。
A. 基于37,680个样本的无权重UniFrac PCoA图，表明QIIME 2的大样本量处理能力(scalable)。按地球微生物组的本体论分类着色。
B. 波动图(volatility plot)展示母乳和奶粉喂养婴儿双歧杆菌丰度随时间的变化。此可视化方法可用于交互挖掘时空特异的特征。
C. 交互式柱状图展示黄石公园热泉不同温度梯度下物种组成。更多可交互式的可控条件，极大的减少了分析工作量。
D. 人类皮肤表面的分子地图。 着色的点代表小分子化妆品硫酸月桂酸钠在人体皮肤上的丰度。样本数据可以在3D模型上交互式可视化，支持空间模式的发现。
图2. 迭代记录数据来源确保分析可重复
简化的示意图展示创建图1c中柱状图分析过程的可追溯图。其它图的可追溯过程见附图1。
代码可用
QIIME 2对所有用户可用，包括商业用途，源代码见 https://github.com/qiime2
在线方法
我们建立一个qiime2的目录对本流程进行初步了解
wd=~/test/qiime2
mkdir $wd
cd $wd提取QIIME2的存档内容
很多QIIME 2新用户困惑的是结果为特殊格式，不可直接查看，使用不方便。
其实，qza和qzv格式就是zip的压缩包，可使用unzip直接解压
# 下载代表性序列(OTU)
wget https://docs.qiime2.org/2018.8/data/tutorials/moving-pictures/rep-seqs.qza
# 解压
unzip rep-seqs.qza
# 查看序列文件前4行
head -4 8dc793b8-7284-462a-8578-6370ffccebdc/data/dna-sequences.fasta是不是觉得QIIME 2的结果很熟悉了，让我们开始全新的可重复计算新时代吧！
>f352c1f1efecf483511c2270aabd0ae6
TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGTAAGACAGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTTTGTGACTGCAAGGCTG
>82e72255267397b777a1afd44ea22755
TACGGAGGATCCAAGCGTTATCCGGAATCATTGGGTTTAAAGGGTCCGTAGGCGGTTTAGTAAGTCAGTGGTGAAAGCCCATCGCTCAACGGTGGAACGGCCATTGATACTGCTAGACTT附图
附图1. QIIME2原理图
附图2. QIIME2界面各类
QIIME 2提供多种使用界面，方便不同计算水平人员使用。
a. 网页QIIME 2 View查看数据或结果工具，用户无需安装软件；这一设计方便团队负责人、医生、决策者探索其他人分析的交互式可视化结果；
b. 喜欢图形界面的用户可使用原生的图型界面QIIME 2 Studio,，无需命令行或编程技巧；
c. 对于熟悉Linux命令行，计算集群使用的用户，推荐使用命令行界面——q2cli；
d. 使用Jupyter Notebooks、对自运化工作流程感兴趣的数据科学家，可使用Python 3接口的artifact API
附图3. QIIME2文档类型和结构
QIIME2存储的数据采用目录结果，称为存档。这些存档为压缩格式，方便数据移动。目录结构有唯一的根目录，并有UUID作为标识。
作者列表
Evan Bolyen1, Jai Ram Rideout1, Matthew R Dillon1, Nicholas A Bokulich1, Christian Abnet2, Gabriel A Al-Ghalith3, Harriet Alexander4,5, Eric J Alm6,7, Manimozhiyan Arumugam8, Francesco Asnicar9, Yang Bai10,11,12, Jordan E Bisanz13, Kyle Bittinger14,15, Asker Brejnrod16, Colin J Brislawn17, C Titus Brown5, Benjamin J Callahan18,19, Andrés Mauricio Caraballo-Rodríguez20, John Chase1, Emily Cope1,21, Ricardo Da Silva20, Pieter C Dorrestein20, Gavin M Douglas22, Daniel M Durall23, Claire Duvallet6, Christian F Edwardson24, Madeleine Ernst20, Mehrbod Estaki25, Jennifer Fouquier26,27, Julia M Gauglitz20, Deanna L Gibson28,29, Antonio Gonzalez30, Kestrel Gorlick1, Jiarong Guo31, Benjamin Hillmann32, Susan Holmes33, Hannes Holste30,34, Curtis Huttenhower35,36, Gavin Huttley37, Stefan Janssen38, Alan K Jarmusch20, Lingjing Jiang39, Benjamin Kaehler37, Kyo Bin Kang20,40, Christopher R Keefe1, Paul Keim1, Scott T Kelley41, Dan Knights32,42, Irina Koester20,43, Tomasz Kosciolek30, Jorden Kreps1, Morgan GI Langille44, Joslynn Lee45, Ruth Ley46,47, Yong-Xin Liu10,11, Erikka Loftfield2, Catherine Lozupone48, Massoud Maher49, Clarisse Marotz30, Bryan D Martin50, Daniel McDonald30, Lauren J McIver35,36, Alexey V Melnik20, Jessica L Metcalf51, Sydney C Morgan52, Jamie Morton30,49, Ahmad Turan Naimey1, Jose A Navas-Molina30,49,53, Louis Felix Nothias20, Stephanie B Orchanian54, Talima Pearson1, Samuel L Peoples55,56, Daniel Petras20, Mary Lai Preuss57, Elmar Pruesse48, Lasse Buur Rasmussen16, Adam Rivers58, Michael S Robeson, II59, Patrick Rosenthal57, Nicola Segata9, Michael Shaffer48,60, Arron Shiffer1, Rashmi Sinha2, Se Jin Song30, John R Spear61, Austin D Swafford54, Luke R Thompson62,63, Pedro J Torres64, Pauline Trinh65, Anupriya Tripathi20,30,66, Peter J Turnbaugh67, Sabah Ul-Hasan68, Justin JJ van der Hooft69, Fernando Vargas66, Yoshiki Vázquez-Baeza30, Emily Vogtmann2, Max von Hippel70, William Walters46, Yunhu Wan2, Mingxun Wang20, Jonathan Warren71, Kyle C Weber58,72, Chase HD Williamson1, Amy D Willis73, Zhenjiang Zech Xu30, Jesse R Zaneveld74, Yilong Zhang75, Qiyun Zhu30, Rob Knight30,54,76, J Gregory Caporaso1,21
单位列表
Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD, USA
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
Department of Population Health and Reproduction, University of California, Davis, CA, USA
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
University of Copenhagen, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, Copenhagen, Denmark
Centre for Integrative Biology, University of Trento, Trento, Italy
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences & John Innes Centre, Beijing, China
University of Chinese Academy of Sciences, Beijing, China
Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
Division of Gastroenterology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
Hepatology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
Department of Population Health & Pathobiology, North Carolina State University, Raleigh, NC, USA
Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
Collaborative mass spectrometry innovation center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, British Columbia, Canada
A. Watson Armour III Center for Animal Health and Welfare, Aquarium Microbiome Project, John G. Shedd Aquarium, Chicago, IL, USA
Department of Biology, University of British Columbia Okanagan, Okanagan, BC, Canada
Computational Bioscience Graduate Program, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA
Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA
Irving K. Barber School of Arts and Sciences, Department of Biology, The University of British Columbia, Kelowna, BC, Canada
Department of Medicine, The University of British Columbia, Kelowna, BC, Canada
Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
Stanford University, Statistics Department, Palo Alto, CA, USA
Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Broad Institute of MIT and Harvard, Cambridge, MA, USA
Research School of Biology, The Australian National University, Canberra, ACT, Australia
Department of Pediatric Oncology, Hematology and Clinical Immunology, Heinrich-Heine University Dusseldorf, Dusseldorf, Germany
Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
College of Pharmacy, Sookmyung Women’s University, Seoul, Republic of Korea
San Diego State University, Department of Biology, San Diego, CA, USA
Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA
Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
Science Education, Howard Hughes Medical Institute, Ashburn, VA, USA
Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
Department of Statistics, University of Washington, Seattle, WA, USA
Department of Animal Science, Colorado State University, Fort Collins, CO, USA
Irving K. Barber School of Arts and Sciences, Unit 2 (Biology), University of British Columbia, Kelowna, BC, Canada
Mountain View, Google LLC, Mountain View, CA, USA
Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
School of Information Studies, Syracuse University, Syracuse, NY, USA
School of STEM, University of Washington Bothell, Bothell, WA, USA
Department of Biological Sciences, Webster University, St Louis, MO, USA
Agricultural Research Service, Genomics and Bioinformatics Research Unit, United States Department of Agriculture, Gainesville, FL, USA
College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
Computational Bioscience Program, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA
Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
Department of Biology, San Diego State University, San Diego, CA, USA
Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
Division of Biological Sciences, University of California San Diego, San Diego, CA, USA
Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, USA
Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
Department of Mathematics, University of Arizona, Tucson, AZ, USA
National Laboratory Service, Environment Agency, Starcross, UK
College of Agriculture and Life Sciences, University of Florida, Gainesville, FL, USA
Department of Biostatistics, University of Washington, Seattle, WA, USA
University of Washington Bothell, School of STEM, Division of Biological Sciences, Bothell, WA, USA
Merck & Co. Inc., Kenilworth, NJ, USA
Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
Reference
https://peerj.com/preprints/27295/
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet C, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope E, Da Silva R, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley G, Janssen S, Jarmusch AK, Jiang L, Kaehler B, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MG, Lee J, Ley R, Liu Y, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton J, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson, II MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CH, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. 2018. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ Preprints 6:e27295v2 https://doi.org/10.7287/peerj.preprints.27295v2
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