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Advances in sequencing, proteomics, transcriptomics, metabolomics, and others are givingus new insights into the microbial world and dramatically improving our abilityto understand their community composition and function at high resolution.These new technologies are generating vast amounts of data, even from a singlestudy or sample, leading to challenges in storage, representation, analysis,and integration of the disparate data types. Qiita was designed to allow usersaddress these new challenges by keeping track of multiple studies with multiple'omics data. Additionally, Qiita is capable of supporting multiple analyticalpipelines through a 3rd-party plugin system, allowing the user to have a singleentry point for all their analyses. Qiita's main site provides database andcompute resources to the global community, alleviating the technical burdens,such as familiarity with the command line or access to compute power, that aretypically limiting for researchers studying microbial ecology.

Qiita is currently in production/stable status. We are very open to communitycontributions and feedback. If you're interested in contributing to Qiita,seeCONTRIBUTING.md.If you'd like to report bugs or request features, you can do that in theQiita issue tracker.

To install and configure your own Qiita server, seeINSTALL.md. However, Qiita is not designed to be used locally but rather on a server, we therefore advise against installing your own version on a personal computer. Nevertheless, it can run just fine on a laptop or small computer for development and educational purposes. For example, for every single PR and release, we install Qiita from scratch as GitHub Actions, you can followthese steps.

For more specific details about Qiita's philosophy and design visitthe Qiita main site tutorial.

• Full study management: Create, delete, update samples in the sample andmultiple preparation information files.
• Upload files via direct drag & drop from the web interface or via scpfrom any server that allows these connections.
• Study privacy management: Sandboxed -> Private -> Public.
• Easy long-term sequence data deposition to the European Nucleotide Archive (ENA),part of the European Bioinformatics Institute (EBI) for private and publicstudies.
• Raw data processing forTarget Gene, Metagenomic, Metabolomic, Genome Isolates and BIOM files. NOTE: BIOM files can be added as new preparation files for downstream analyses; however, this cannot be made public in the system.
• Basic downstream analyses using QIIME 2. Note that Qiita produces qza/qzv in the analytical steps but you can also convertnon QIIME 2 artifacts.
• Bulk download ofstudies and artifacts.
• Basic study search in the study listing page.
• Complex metadata search via redbiom.

For more detailed information visit theQiita tutorialand theQiita help.

• Multiplexed SFF
• Multiplexed FASTQ: forward, reverse (optional), and barcodes
• Per sample FASTQ: forward and reverse (optional)
• Multiplexed FASTA/qual files
• Per sample FASTA, only for "Full Length Operon"