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edamame-course
tutorials/illumina_overview_tutorial
README.md

README.md

Haruo Suzuki (haruo[at]g-language[dot]org)
Last Update: 2018-01-13


QIIME Tutorial Project

Project started 2016-12-12 at BH16.12.

We have created shell scripts to perform all analyses in QIIME tutorials.

http://qiime.org/tutorials/

Project directories

qiime/
 README.md: project documentation
 edamame-course/: contains edamame-course/Amplicon_Analysis
 tutorials/: contains QIIME Tutorials / Illumina Overview Tutorial

Steps

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

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

tutorials

本家QIIME Tutorials

Illumina Overview Tutorial

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

454 Overview Tutorial

wget ftp://ftp.microbio.me/pub/qiime-files/qiime_overview_tutorial.zip
unzip qiime_overview_tutorial.zip 
cd qiime_overview_tutorial

Run environment

$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)

Updates

2016-12-13

edamame-course/Amplicon_Analysis downloaded on 2016-12-13 using:

git clone https://github.com/edamame-course/Amplicon_Analysis

Tools

2016-12-12

Install Anaconda

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"

Install QIIME

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

References

QIIME

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.

Galaxy

https://galaxyproject.org/galaxy-updates/2017-06/#qiime-and-mothur Qiime and mothur

Japanese

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

MetaSUB


http://wiki.pitagora-galaxy.org/wiki/index.php/Workflow_Qiime

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