Welcome to Qiita’s documentation!

Qiita (canonically pronounced cheetah) is a software package intended for analysis and administration of multi-omics datasets.

Qiita provides a free and open platform for users to:

1. Easily share and reuse existing data-sets in the form of studies.

2. Perform analyses (by combining one or more studies/data-sets) using published and unpublished data that meet the standards as described by this documentation.

3. Easily interface with the EBI repository for automated deposition. Query and interact with Qiita data programmatically.

Beginner’s Guides: The latests tutorials can be found in: CMI Qiita/GNPS workshop pages.

Looking for information about getting started? Please see the document here:

• Getting Started Guide
  • Creating an Account
    • Home Screen
  • Creating a Study
    • Editing a Study
    • Example files
    • Sample information file
    • Required fields for Qiita
    • Required fields for EBI submission and to make a study public
  • Attaching the Sample Information to the Study
    • Upload Sample Information
    • Attach Sample Information
    • Viewing Sample Information
    • Update Sample info
  • Creating and Working With Preparation information
    • Prepare information files
    • Example files
    • Required fields for Qiita
    • Required fields for pre-processing target gene data
  • Attaching Preparation Information to the Study
    • Upload Prep Information
    • Attach Prep Information
    • Associate Data with Prep Information
    • Update prep info
• Qiita Philosophy
  • Plugin ideology
  • A Study
  • Qiita allows for complex study designs
  • Portals

Looking for information about how to process your data? Please see the document here:

• Processing Data
  • Processing Network Page
    • Files Network Within Data Type
  • Processing Recommendations
    • Processing recommendations
      • Target gene barcoded sequencing
        • Sequencing deblur (preferred)
        • Sequencing clustering
      • The Sequencing Processing Pipeline (SPP)
      • Shotgun sequencing
        • Wolka and Bowtie2 using Read Pairing Schemes
          • Summary
          • Alignment parameters
          • Synthetic data
        • Adapter and host filtering
        • Aligners
        • Reference databases
      • Metatranscriptome processing
        • Sample processing guidelines for metatranscriptomic data
        • Ribosomal read filtering
        • Building Custom databases
        • SortMeRNA Usage
      • Genome Isolate Processing
  • Converting Data to BIOM Tables
    • BIOM
    • FASTQ, SFF, FNA/QUAL, or FASTA/QUAL Files
  • Deblurring
    • Deblur quality filtering
      • Methods
      • Results
      • Discussion
    • deblur version 2021.09
      • How do I know if my study processing had this bug?
      • Sample counts implications
      • How perversive is this bug?
      • Reaching out to affected study owners
  • Closed-Reference OTU Picking
  • Woltka / bowtie2 paired-end
    • Wolka and Bowtie2 using Read Pairing Schemes
      • Summary
      • Alignment parameters
      • Synthetic data

Looking for information about submitting your files to EBI? Please see the document here:

• Making data Public in Qiita and/or send data to EBI-ENA
  • EBI-ENA NULL values vocabulary
  • Checklist
• Earth Microbiome Project Ontology (EMPO)
  • EMPO 1 (first release)

Looking for comparable studies? Please see the document here:

• redbiom
  • Search Options

Looking for information about analyzing your data? Please see the document here:

• Analyzing Samples
  • Qiita now uses QIIME2 plugins for analysis.
  • Creating A New Analysis
  • Single vs. Meta Analysis
  • Processing Network Page: Commands
    • Rarefying Features
    • Filtering Samples by Metadata
    • Summarizing Taxa
    • Calculating Alpha Diversity
    • Calculating Beta Diversity
    • Calculating Alpha Correlation
    • Performing Principal Coordinate Analysis
    • Calculating Beta Group Significance
    • Calculating Beta Correlation
  • Processing Network Page: Results
    • Taxa Bar Plot
    • Alpha Diversity Box Plots and Statistics
    • Alpha Correlation Box Plots and Statistics
    • Beta Diversity Distance Matrix
    • Principal Coordinate Analysis Plot
    • Beta Group Significance Box Plots and Statistics
    • Beta Correlation

Interested in how you can access and use public data available on Qiita? Please see the document here:

• Introduction to the download and (re)analysis of public data from Qiita
  • Retrieving Public Data for Own Analysis
    • Introduction
    • Set up
    • Introduction to the example data
    • Retrieving Data
      • Contexts
        • An explanation of contexts in redbiom and Qiita.
          • Obtaining Data
          • Sequencing techniques
          • Region sequenced for species identification
            • Marker genes versus whole genome
          • Processing Data
            • Assigning sequences to taxa
          • Conclusion
          • Bibliography
      • Commands to retrieve data
        • Retrieving data using the redbiom plug-in within Qiita
        • Retrieving data with redbiom in the command line
    • Conclusion
    • Bibliography
  • Processing Public Data Retrieved with redbiom
    • Introduction
    • Set up
    • Command line workflow
    • Python Workflow
      • Set up
      • Load and process data
    • Conclusion
    • Bibliography
  • Statistical Analysis to Justify Clinical Trial Sample Size Tutorial
    • Set up
    • Find and process data in Qiita
    • Retrieve artifacts/data from Qiita and create figures
      • Download data from Qiita
    • Python workflow
      • Set up environment
      • Process the artifact data
      • Create Figures
    • R studio workflow
      • Set up environment
      • Import and process data
      • Make Plots
    • Conclusion
    • Bibliography

Looking for available guides? Please see these documents:

• Qiita Guides
  • Study and analysis sharing
    • Sharing a Study
    • Sharing an Analysis
  • No raw sequences
    • Per sample FASTQ files with barcode information
    • Per sample FASTQ files without barcode and primer information
    • Per sample FASTQ files without barcode but with primer information
  • Join paired end reads
    • Joining forward and reverse reads for raw files
    • Joining forward and reverse reads for per sample FASTQ files without barcodes and primers
    • Per sample FASTQ files without barcodes but with primer information with overlapping regions
  • Templates
• Frequently Asked Questions
  • Qiita data disclaimer
  • What kind of data can I upload to Qiita for processing?
  • What’s the difference between a sample and a prep information file?
  • How should I split my samples within preparations?
  • Example study processing workflow
  • How to solve download or unzip errors?
  • Do you have specific Qiita questions?
  • Do you have general analytical questions?
  • Do you have Meta-Analysis questions?
  • How to solve BIOM name errors?
  • What’s a Qiita Artifact?
  • How to convert Qiita files to QIIME2 artifacts?
  • How to add extra files to a Qiita study?
  • Where’s my QIIME1 mapping file?
  • I want to transfer a lot of files to Qiita, is there an easy way?
  • How do I update the sample or preparation file?
  • When do I need the run_prefix in my preparation information file?
  • Software and Data Licensing
  • Some of the studies have Qiita-EBI Import as the PI, why is this?
  • Are you planning a workshop or class?
  • How to cite Qiita?
• Downloading From Qiita
  • Downloading All Public Data in BIOM format
  • Download Processed Data
  • Download Analyzed Data
  • Access a public study or artifact without login
  • Access non-public artifacts without a login
  • Download metadata, raw or all BIOM files from a study
  • Finding Samples Based On Their Metadata
  • Moving Your Analysis From Qiita to QIIME2
• Glossary
• References

If you intend to deploy or develop Qiita we recommend that you have a look at the following documents:

• Administrator Tutorials
  • User Portals
    • Creating/Deleting a portal
    • Adding/Deleting studies on a portal
    • Adding/Deleting analyses on a portal
    • Customizing portal text and style
• Developer Tutorials
  • Qiita Plugins
    • Overview of Qiita’s plugin system
    • Developing a Qiita Plugin
  • Qiita REST API
    • Qiita Plugin REST API
    • Qiita Internal REST API
  • Qiita’s per job resources allocation
    • Job types
    • Resources allocation
    • Resources allocation by formula
  • Qiita Workflows
    • How to add a workflow?