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:
- Easily share and reuse existing data-sets in the form of studies.
- Perform analyses (by combining one or more studies/data-sets) using published and unpublished data that meet the standards as described by this documentation.
- 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
- Creating a Study
- Creating and Working With Sample information
- Attaching the Sample Information to the Study
- Creating and Working With Preparation information
- Attaching Preparation Information to the Study
- Qiita Philosophy
Looking for information about how to process your data? Please see the document here:
- Processing Data
- Processing Network Page
- Processing Recommendations
- Processing recommendations
- Target gene barcoded sequencing
- Shotgun sequencing
- Metatranscriptome processing
- Genome Isolate Processing
- Processing recommendations
- Converting Data to BIOM Tables
- Closed-Reference OTU Picking
Looking for information about submitting your files to EBI? Please see the document here:
Looking for comparable studies? Please see the document here:
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
- Processing Network Page: Results
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
- Set up
- Introduction to the example data
- Retrieving Data
- Commands to retrieve data
- Processing Public Data Retrieved with redbiom
- Statistical Analysis to Justify Clinical Trial Sample Size Tutorial
Looking for available guides? Please see these documents:
- Qiita Guides
- Study and analysis sharing
- No raw sequences
- Join paired end reads
- 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?
- 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
If you intend to deploy or develop Qiita we recommend that you have a look at the following documents:
- Administrator Tutorials
- Developer Tutorials