QIIME 2用户文档. 17鉴定和过滤嵌合体序列q2-vsearch(2019.7)

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前情提要

鉴定和过滤嵌合体序列q2-vsearch

Identifying and filtering chimeric feature sequences with q2-vsearch

https://docs.qiime2.org/2019.7/tutorials/chimera/

注：最好按本教程顺序学习，想直接学习本章，至少完成本系列《1简介和安装》。

在QIIME 2中进行嵌合体检验基于FeatureTable[Frequency]和FeatureData[Sequences]对象。QIIME 2内嵌了vsearch的Uchime无参(de novo)和有参(reference)去嵌合体流程。对于此过程的细节，详见Uchime的论文和vsearch的帮助文档。(推荐USEARCH软件主页有比较详细的教程，vsearch帮助读起来不方便)

本节使用《6沙漠土壤分析Atacama soil》中的特征表。

数据下载

Obtain the data

mkdir -p qiime2-chimera-filtering-tutorial
cd qiime2-chimera-filtering-tutorial

wget -c \
  -O "atacama-table.qza" \
  "https://data.qiime2.org/2019.7/tutorials/chimera/atacama-table.qza"

wget -c \
  -O "atacama-rep-seqs.qza" \
  "https://data.qiime2.org/2019.7/tutorials/chimera/atacama-rep-seqs.qza"

无参嵌合体鉴定

Run de novo chimera checking

# 7s
time qiime vsearch uchime-denovo \
  --i-table atacama-table.qza \
  --i-sequences atacama-rep-seqs.qza \
  --output-dir uchime-dn-out

输入对象:

注：基于参考序列(有参，Reference-based)的嵌合体鉴定方法详见vsearch uchime-ref

可视化统计结果

Visualize summary stats

qiime metadata tabulate \
  --m-input-file uchime-dn-out/stats.qza \
  --o-visualization uchime-dn-out/stats.qzv

输入可视化:

过滤特征表和序列

Filter input tables and sequences

过滤嵌合体和可疑序列

Exclude chimeras and “borderline chimeras”

qiime feature-table filter-features \
  --i-table atacama-table.qza \
  --m-metadata-file uchime-dn-out/nonchimeras.qza \
  --o-filtered-table uchime-dn-out/table-nonchimeric-wo-borderline.qza
qiime feature-table filter-seqs \
  --i-data atacama-rep-seqs.qza \
  --m-metadata-file uchime-dn-out/nonchimeras.qza \
  --o-filtered-data uchime-dn-out/rep-seqs-nonchimeric-wo-borderline.qza
qiime feature-table summarize \
  --i-table uchime-dn-out/table-nonchimeric-wo-borderline.qza \
  --o-visualization uchime-dn-out/table-nonchimeric-wo-borderline.qzv

输出对象:

  • uchime-dn-out/rep-seqs-nonchimeric-wo-borderline.qza：过滤嵌合体的序列。 查看 | 下载
  • uchime-dn-out/table-nonchimeric-wo-borderline.qza：过滤嵌合体的特征表。 查看 | 下载

输出可视化结果:

  • uchime-dn-out/table-nonchimeric-wo-borderline.qzv：特征表统计。 查看 | 下载

过滤嵌合但保留可疑序列

Exclude chimeras but retain “borderline chimeras”

qiime feature-table filter-features \
  --i-table atacama-table.qza \
  --m-metadata-file uchime-dn-out/chimeras.qza \
  --p-exclude-ids \
  --o-filtered-table uchime-dn-out/table-nonchimeric-w-borderline.qza
qiime feature-table filter-seqs \
  --i-data atacama-rep-seqs.qza \
  --m-metadata-file uchime-dn-out/chimeras.qza \
  --p-exclude-ids \
  --o-filtered-data uchime-dn-out/rep-seqs-nonchimeric-w-borderline.qza
qiime feature-table summarize \
  --i-table uchime-dn-out/table-nonchimeric-w-borderline.qza \
  --o-visualization uchime-dn-out/table-nonchimeric-w-borderline.qzv

输出对象:

  • uchime-dn-out/table-nonchimeric-w-borderline.qza：过滤嵌合体的序列。 查看 | 下载
  • uchime-dn-out/rep-seqs-nonchimeric-w-borderline.qza：过滤嵌合体的特征表。 查看 | 下载

输出可视化结果:

  • uchime-dn-out/table-nonchimeric-w-borderline.qzv：特征表统计。 查看 | 下载

Reference

https://docs.qiime2.org/2019.7

Evan Bolyen*, Jai Ram Rideout*, Matthew R. Dillon*, Nicholas A. Bokulich*, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, Eric J. Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E. Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J. Brislawn, C. Titus Brown, Benjamin J. Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily K. Cope, Ricardo Da Silva, Christian Diener, Pieter C. Dorrestein, Gavin M. Douglas, Daniel M. Durall, Claire Duvallet, Christian F. Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M. Gauglitz, Sean M. Gibbons, Deanna L. Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin A. Huttley, Stefan Janssen, Alan K. Jarmusch, Lingjing Jiang, Benjamin D. Kaehler, Kyo Bin Kang, Christopher R. Keefe, Paul Keim, Scott T. Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G. I. Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D. Martin, Daniel McDonald, Lauren J. McIver, Alexey V. Melnik, Jessica L. Metcalf, Sydney C. Morgan, Jamie T. Morton, Ahmad Turan Naimey, Jose A. Navas-Molina, Louis Felix Nothias, Stephanie B. Orchanian, Talima Pearson, Samuel L. Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S. Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R. Spear, Austin D. Swafford, Luke R. Thompson, Pedro J. Torres, Pauline Trinh, Anupriya Tripathi, Peter J. Turnbaugh, Sabah Ul-Hasan, Justin J. J. van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C. Weber, Charles H. D. Williamson, Amy D. Willis, Zhenjiang Zech Xu, Jesse R. Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight & J. Gregory Caporaso#. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology. 2019, 37: 852-857. doi:10.1038/s41587-019-0209-9

译者简介

刘永鑫，博士。2008年毕业于东北农大微生物学，2014年于中科院遗传发育所获生物信息学博士，2016年博士后出站留所工作，任宏基因组学实验室工程师。目前主要研究方向为宏基因组数据分析和植物微生物组，QIIME 2项目参与人。目前在Science、Nature Biotechnology等杂志发表论文十余篇。2017年7月创办“宏基因组”公众号，目前分享宏基因组、扩增子原创文章400余篇，代表博文有《扩增子图表解读、分析流程和统计绘图三部曲(21篇)》、《Nature综述：手把手教你分析菌群数据(1.8万字)》、《QIIME2中文教程(18篇)》等，关注人数6.5万+，累计阅读1000万+。

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