Haruo Suzuki (haruo[at]g-language[dot]org)
Last Update: 2018-01-13
Project started 2016-12-12 at BH16.12.
We have created shell scripts to perform all analyses in QIIME tutorials.
qiime/
README.md: project documentation
edamame-course/: contains edamame-course/Amplicon_Analysis
tutorials/: contains QIIME Tutorials / Illumina Overview Tutorial
login to your server with ssh -X or ssh -Y (X11 forwarding)
ssh -X username@remote_host
Clone the latest version of the repository:
git clone https://github.com/haruosuz/qiime
Start QIIME:
source activate qiime1
Finish QIIME:
source deactivate
edamame-course/Amplicon_Analysis
Run the driver scripts in the directory edamame-course/ with:
bash run.2016-07-13-QIIME1.sh
# This step will take about 80 minutes
bash run.2016-07-13-QIIME2.sh
# This step will take about 15 minutes
bash run.2016-07-13-QIIME3.sh
# This step will take about 5 minutes
Run the driver script in the directory tutorials/illumina_overview_tutorial/ with:
bash run_illumina_overview_tutorial.sh
# This step will take about 35 minutes
wget ftp://ftp.microbio.me/pub/qiime-files/qiime_overview_tutorial.zip
unzip qiime_overview_tutorial.zip
cd qiime_overview_tutorial
$uname -a
Linux neo 3.10.0-327.18.2.el7.x86_64 #1 SMP Thu May 12 11:03:55 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
$cat /etc/redhat-release
CentOS Linux release 7.2.1511 (Core)
$cat /proc/version
Linux version 3.10.0-327.18.2.el7.x86_64 (builder@kbuilder.dev.centos.org) (gcc version 4.8.3 20140911 (Red Hat 4.8.3-9) (GCC) ) #1 SMP Thu May 12 11:03:55 UTC 2016
$python --version
Python 2.7.12 :: Anaconda 4.2.0 (64-bit)
2016-12-13
edamame-course/Amplicon_Analysis downloaded on 2016-12-13 using:
git clone https://github.com/edamame-course/Amplicon_Analysis
2016-12-12
Anaconda 4.2.0 For Linux | Python 2.7 version | 64-BIT INSTALLER (446M) was downloaded from [Download for Linux] tab at https://www.continuum.io/downloads and installed on 2016-12-12 using:
wget https://repo.continuum.io/archive/Anaconda2-4.2.0-Linux-x86_64.sh
bash Anaconda2-4.2.0-Linux-x86_64.sh
# [/home/haruo/anaconda2] >>>
At the end of ~/.bashrc file:
# added by Anaconda2 4.2.0 installer
export PATH="/home/haruo/anaconda2/bin:$PATH"
QIIME Installation Guide — Homepage
Installed QIIME on 2016-12-12 using:
# Create your qiime1 environment and install QIIME
conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda
# Activate your qiime1 environment and test your QIIME installation
source activate qiime1
print_qiime_config.py -t
https://www.ncbi.nlm.nih.gov/pubmed/29688343 FEMS Microbiol Lett. 2018 May 1;365(10). doi: 10.1093/femsle/fny104. A town on fire! Integrating 16S rRNA gene amplicon analyses into an undergraduate microbiology lecture class. Tobin TC1, Shade A2.
https://forum.qiime2.org/t/tutorial-integrating-qiime2-and-r-for-data-visualization-and-analysis-using-qiime2r/4121 Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R - Community Contributions / Tutorials - QIIME 2 Forum
https://www.ncbi.nlm.nih.gov/pubmed/27924593 Methods Mol Biol. 2017;1537:153-163. Analysis of 16S rRNA Gene Amplicon Sequences Using the QIIME Software Package. Lawley B1, Tannock GW2.
- Apr 28, 2016 alexcritschristoph/Qiime16sTutorial: A tutorial on up-to-date methods of 16S analysis with QIIME
- Jul 15, 2016 QIIME 2 Self documenting, Extensible, and Reproducible Microbiome Analysis in Python 3 | SciPy 201 - YouTube
- 2016/01/12 mothur and QIIME
- 2015/09/ [PDF]Workflow from sample to analyzed data – uses Qiime for analysis
- 2014 Analyzing Metagenomic Data with QIIME
- 2013+ Learning QIIME - Werner Lab
- 2013+ EDAMAME : Intro to QIIME
- 2011-2013, Analyzing metagenomes with QIIME — PICRUSt 1.1.0 documentation
- 2011+ LEfSe · An Introduction to QIIME 1.9.1
https://galaxyproject.org/galaxy-updates/2017-06/#qiime-and-mothur Qiime and mothur
- QIIME Contribution Fest - 9th & 10th January 2017 · Issue #1078 · galaxyproject/tools-iuc
- QIIME 1.9.1 Galaxy Wrapper - Galaxy Tool Shed / (sandbox for testing)
- Jun 26 QIIME 1.9.1 Galaxy Wrapper
- Jun 7 problems with qiime integration on galaxy - Google Groups
- 2016-05-19 Galaxy Development List Archive - Update on Qiime in Galaxy?
- 2015-11-30 WIP: Add Qiime wrappers #431
- 2015-11-25 CeSGO - Group: Galaxy User Group Grand Ouest ~ Wiki: Metagenomics Remote Hackathon
- 2015-10-22 QIIME on Galaxy - Google Groups
- 2015-07 GCC2015 Posters P07: 16S rDNA amplicon sequencing data analysis in Galaxy
- 2015-03-27 QIIME-Galaxy
- 2012 JA Navas Molina 著 Develop a Galaxy-based Graphic User Interface for QIIME
日本語資料
http://staffblog.amelieff.jp/entry/2017/12/01/154644 QIIME2のはなし。 - アメリエフのブログ
http://pediatricsurgery.hatenadiary.jp/entry/2017/11/19/200241 mothur開発者によるmothurとQIIMEの比較 - Note of Pediatric Surgery
http://bioinformatic-r-and-me.blogspot.com/2017/10/qiime.html バイオインフォマティクスとRとわたし: QIIMEインストールのやり方
- 2016/11/26 Qiime v1.9.0
- 2016/04/14 細菌群集の特徴付けのための効率的な核酸抽出および16S rRNAの遺伝子配列決定
- 2016/03/14 次世代シークエンサーデータ解析ツール — 東京大学 味埜・佐藤研究室 OTUMAMiを用いた16SrRNAシークエンスデータ解析
- 2012 佐藤弘泰 著 次世代シーケンサーが照らし出す排水処理微生物生態系
- 2015-07-25 USEARCHを使った16S rRNAメタゲノムデータの分析 - yokaのblog
- 2015-06-30 QIIMEの実行時エラー ft2font.so: undefined symbol: PyUnicodeUCS4_AsEncodedString | 2015-06-23 QIIMEの実行時のエラー PyUnicodeUCS2_AsASCIIString - 備忘録 the next generation
- 2017-01-14 2015-03-11 Qiime 1.9 - Qiita
- 2015-01-27 mac Qiimeのインストール | Note of Pediatric Surgery 予測メタゲノム HUMAnN
- 2013-06-11 Qiimeのアップデートを行いました | 2012-10-04 Qiimeを動かしてみました - Takeruでこのようなものを動かしてみました
- 2010/03/02 次世代シーケンサーを用いた菌叢解析 (16S rRNA 遺伝子 PCR サンプルの解析) - 製品評価技術基盤機構
- 次世代シーケンス・アンプリコンデータ解析(帰属分類群の推定) | RDPおよび独自データベースを利用した解析
- Qiime - Draft of Pediatric Surgery
- 2017-03-13 16S rRNA遺伝子解析の限界と予測メタゲノム解析 - Piphillinの導入 - Note of Pediatric Surgery
- Bioinformatics Analysis – MetaSUB
- urban metagenome
- Boston Subway Microbiome | ENA PRJNA301589
- New York Subway Microbiome | ENA PRJNA271013
http://wiki.pitagora-galaxy.org/wiki/index.php/Workflow_Qiime