QiimeReporter is a straightforward pipeline for the analysis of amplicon sequences directly from raw Illumina paired-end data. It integrates the main Qiime2 commands with R in order to generate a final html report that can be opened in any web browser and easily shared between researchers.
QiimeReporter has been developed as a Conda environment to make things easier.
Miniconda provides the Conda environment and package manager, and is the recommended way to install QiimeReporter:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
conda update conda
Once you have Miniconda installed, run the following commands to install QiimeReporter:
conda create -n qiimereporter
conda activate qiimereporter
conda install -c dabadgarcia qiimereporter
qiimereporter-setup
usage: qiimereporter <options>
OBLIGATORY OPTIONS:
-i/--input Path to the directory where the raw reads are located
-m/--metadata Path to the file with the metadata regarding the samples
The file must have an specific organization for the program to work
If you don't have any or you would like to have an example or extra information,
please type:
$0 example-metadata
-o/--output Path and name of the output directory
OTHER OPTIONS:
--citation Show citation
--color Color multivariate analysis from a categorical variable in sample-metadata
-d/--database Path to prefered database, must be .qza file (default SILVA132)
--depth Minimun number of reads for a sample to be included in the rarefaction figure
-f/--forward Truncates length of the forward reads (default='0')
--group Column number of the variable in sample-metadata to group the taxa-bar-plot
-h/--help Show this help
--no-diversity Excludes the diversity index figures from the report
--no-heatmap Excludes the heatmap from the report
--no-network Excludes the network from the report
--no-pcoa Excludes the pcoa figures from the report
--no-rarefactionExcludes the rarefaction curves from the report
--multivariate Includes other multivariate analysis in the report (NMDS, DCA, CCA, RCA)
--report-only To generate only html report document, must be executed in the report_files directory
-r/--reverse Truncates length of the reverse reads (default='0')
-t/--threads Number of threads to use (default=$CPUS) <integer>
--title Path to a file containing the title of the report, avoid using special characters
QiimeReporter will use a default title if this option is not passed
-v/--version Show version
Example:
qiimereporter -i raw_reads -m sample-metadata.tsv --output output_folder -t 32
A Qiime2 metadata text file is needed for QiimeReporter to work by using the -m/--metadata option. This file will include all the information regarding the sample and requires an specific organization:
- Columns must be tab separated
- First row:
- First column must me called "#SampleID" and harbor samples names (avoid special characters)
- Second column must be called "BarcodeSequence" and should be left blank
- Third column must be called "LinkerPrimerSequence" and should be left blank
- Fourth (and so on) columns are descriptive. They are no needed for the program but the information will be used and appear in the report. Add as much as needed
- Second row:
- First column must me called "#q2:types" and specifies type of variable for each column
- Columns should be clasiffied into "categorical" if they are non-numeric values and "numeric" if the column consists only of numbers. Missing data (i.e. empty cells) are supported in categorical columns as well as numeric columns
- First row:
If you type qiimereporter example-metadata, a Qiime2 template file called sample-metadata.tsv will be created in your working directory. You can also download the file here. More information about metadata can be found here.
QiimeReporter stores every file generated during the analysis in three different directories, all of them included within the main output directory specified with the -o/--output option:
- complete_taxonomy_otutables: the otu tables with the complete taxonomy for the six main leves of SILVA.
- qiime2_artifacts: all the artifacts produced during the analysis with Qiime2.
- report_files: the files used to generate the report with R.
Once the analysis is finished, QiimeReporter summarizes the results in a interactive html report in your output directory. An example of the report file can be visualized here.
Previous Qiime2 users can convert their results to be used with QiimeReporter.
usage: qiimereporter-format <options>
OBLIGATORY OPTIONS:
-i/--input Path to the directory where the files are located
-m/--metadata Path to the Qiime2 metadata file
OTHER OPTIONS:
-t/--threads Number of threads to use if tree option is passed (default=$CPUS) <integer>
--tree Pass this option to create a tree
Please be sure that stats-dada2.qza, table.qza, taxonomy.qza, and tree.nwk are in the input directory
before proceeding
If you have not created the tree, please also copy the rep-seqs.qza file into the input directory
and pass the option --tree
After formatting is completed, you should run qiimereporter with the option --report-only to create the html report.
Example:
qiimereporter-format -i qiime2_files -m sample-metadata.tsv -t 32
qiimereporter --report-only
If you use QiimeReporter before publication is released, please cite as:
David Abad, Narciso M. Quijada and Marta Hernandez. QiimeReporter. (2019) https://github.com/dabadgarcia/qiimereporter
Users are also highly encouraged to cite Qiime2 and R when using QiimeReporter.
QiimeReporter is a open-source software licensed under GPLv3.