Qiita: Spot Patterns

microbiome, microbiome-analysis, python
pip install qiita-spots==0.2.0


Qiita (canonically pronounced cheetah)

Build Status Coverage Status Gitter

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

Qiita is currently in alpha status. We are very open to community contributions and feedback. If you're interested in contributing to Qiita, see CONTRIBUTING.md. If you'd like to report bugs or request features, you can do that in the Qiita issue tracker.

To install and configure your own Qiita server, see INSTALL.md.

For more specific details about qiita visit the Qiita main site tutorial.

Current features

  • Create a study, add a sample information file with the description (metadata, clinical, geographical, etc) of each sample and multiple preparation information files, how the samples were prepared in the wet lab prior to data generation.
  • Update sample information by modifying values in the existing columns, via an upload and processing of a new information file. Updates include being able to change values in existing columns or add new ones. It is also possible to add samples to an existing sample information sheet. We currently don't support deletions.
  • Change the status of a study: Sandboxed -> Private -> Public.
  • Long term sequence data deposition to the European Nucleotide Archive (ENA), part of the European Bioinformatics Institute (EBI).
  • Search over existing studies (see known issues).
  • Generate basic visualizations with the available studies and datasets.

Accepted raw files

  • Multiplexed SFF
  • Multiplexed FASTQ: forward, reverse (optional), and barcodes
  • Per sample FASTQ: forward
  • Multiplexed FASTA/qual files

Known issues

  • The metadata search is broken
  • Analysis will fail for non 16S datasets and/or multiple processed data from the same study
  • https is down for *.microbio.me


The following is a non-exhaustive list of features that we plan to add in the future.

  • Allow to update any kind of biom for data analysis and visualization
  • Integration of other pipelines via artifacts. Processing of raw data in external sources. For example, metabolomics processing in GNPS and data visualization in Qiita.
  • Creation of a REST API to query and access the data hosted by Qiita.
  • Improved analysis pipeline for target gene datasets.
  • Crowd-sourced metadata curation of existing studies: improve the metadata of existing studies by submitting “fix proposals” to the authors of the study.