q2-summarizer

QIIME2 plugin for generating interactive summary data

Example report

http://htmlpreview.github.io/?https://github.com/twbattaglia/q2-summarizer/blob/master/example/index.html

Installation

See https://github.com/qiime2/qiime2/wiki/Installing-and-using-QIIME-2 for more information on how to set up a qiime2 environment

# Activate qiime2 conda environment
source activate q2test

# Install plugin from github
pip install https://github.com/twbattaglia/q2-summarizer/zipball/master.zip

# Check plugin was installed
qiime info

# Check plugin is working correctly
qiime summarizer --help

Usage

Download and convert example OTU-table

# Download example (.biom) file
curl -sO https://dl.dropboxusercontent.com/u/2868868/data/qiime2/feature-table.biom

# Convert biom table to QIIME2 Artifact
qiime tools import --type "FeatureTable[Frequency]" --input-path feature-table.biom --output-path feature-table-frequency.qza

Run summarizer on OTU-table to generate an interactive report

# Run summarizer on an otu-table
qiime summarizer otu-table --i-table feature-table-frequency.qza --o-visualization summarize_out

# View results
qiime tools view summarize_out.qzv

Future/Current features

• fastq-reads : Summarize raw fastq files.
• joined-pe : Summarize after merging PE reads.
• split-libraries : Summarize after de-multiplexing.
• otu-picking : Summarize after OTU-picking/other methods.
• otu-table : Summarize an OTU-table with absolute counts.

History

TODO: Write history

Credits

• Qiime2 https://github.com/qiime2/qiime2
• AdminLTE https://github.com/almasaeed2010/AdminLTE