diff --git a/source/_old_docs_warning.rst b/source/_old_docs_warning.rst new file mode 100644 index 00000000..719dfbf9 --- /dev/null +++ b/source/_old_docs_warning.rst @@ -0,0 +1,14 @@ +.. warning:: + This site has been replaced by the new QIIME 2 "amplicon distribution" documentation, as of the 2025.4 release of QIIME 2. + You can still access the content from the "old docs" here for the QIIME 2 2024.10 and earlier releases, but we recommend that you transition to the new documentation at https://amplicon-docs.qiime2.org. + **Content on this site is no longer updated and may be out of date.** + + Are you looking for: + + - the QIIME 2 homepage? That's https://qiime2.org. + - learning resources for microbiome marker gene (i.e., amplicon) analysis? See the `QIIME 2 amplicon distribution documentation `_. + - learning resources for microbiome metagenome analysis? See the `MOSHPIT documentation `_. + - installation instructions, plugins, books, videos, workshops, or resources? See the `QIIME 2 Library `_. + - general help? See the `QIIME 2 Forum `_. + + **Old content beyond this point...** 👴👵 \ No newline at end of file diff --git a/source/_templates/action.rst b/source/_templates/action.rst index 66bf7633..b296d6b5 100644 --- a/source/_templates/action.rst +++ b/source/_templates/action.rst @@ -1,3 +1,5 @@ +.. include:: ../../../_old_docs_warning.rst + {{ title }} {{ '=' * title|length }} diff --git a/source/_templates/available.rst b/source/_templates/available.rst index cacb1992..070f3517 100644 --- a/source/_templates/available.rst +++ b/source/_templates/available.rst @@ -1,6 +1,8 @@ Available plugins ================= +.. include:: ../../_old_docs_warning.rst + QIIME 2 microbiome analysis functionality is made available to users via plugins. The following official plugins are currently included in QIIME 2 train releases: .. toctree:: diff --git a/source/_templates/plugin.rst b/source/_templates/plugin.rst index b2b1da9d..87005fac 100644 --- a/source/_templates/plugin.rst +++ b/source/_templates/plugin.rst @@ -1,3 +1,5 @@ +.. include:: ../../../_old_docs_warning.rst + {{ title }} {{ '=' * title|length }} diff --git a/source/about.rst b/source/about.rst index dc5809ba..9808bb01 100644 --- a/source/about.rst +++ b/source/about.rst @@ -1,6 +1,8 @@ What is QIIME 2? ================ +.. include:: _old_docs_warning.rst + QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features: diff --git a/source/citation.rst b/source/citation.rst index dfc8ca50..c11f7cf5 100644 --- a/source/citation.rst +++ b/source/citation.rst @@ -1,6 +1,8 @@ Citing QIIME 2 ============== +.. include:: _old_docs_warning.rst + Please note that almost all QIIME 2 plugins implement methods that were developed independently of the QIIME 2 framework, which should be cited in addition to the QIIME 2 framework itself. This information can be extracted as described below. If you use QIIME 2 in your research, please cite the following `paper`_: @@ -35,7 +37,7 @@ Each time any action is performed in QIIME 2, that information is logged in the 2. Click on the "Provenance" tab in the upper right-hand corner of the browser window. 3. Click on the "Citations" tab that appears in the window below to view a list of citations. 4. Click "Download" to download the list in BibTeX format. -5. Review the citations list and use common sense to make sure that you are citing all software and methods appropriately. If you notice any discrepancies in the citations that are listed by any QIIME 2 plugin, please verify which plugin/action is missing citations or mis-citing, using the directions above for retrieving plugin-specific citation information. Then get in touch on the `QIIME 2 forum`_ to let us know! +5. Review the citations list and use common sense to make sure that you are citing all software and methods appropriately. If you notice any discrepancies in the citations that are listed by any QIIME 2 plugin, please verify which plugin/action is missing citations or mis-citing, using the directions above for retrieving plugin-specific citation information. Then get in touch on the QIIME 2 Forum to let us know! Example methods descriptions @@ -72,5 +74,4 @@ This methods section was adapted from `Pearson et al. 2019`_ (and shortened in t .. _paper: https://doi.org/10.1038/s41587-019-0209-9 .. _VSEARCH: https://github.com/torognes/vsearch .. _q2-feature-classifier: https://doi.org/10.1186/s40168-018-0470-z -.. _QIIME 2 forum: https://forum.qiime2.org/ .. _Pearson et al. 2019: https://doi.org/10.1002/cam4.1965 diff --git a/source/community.rst b/source/community.rst index 05bdf56d..8ac36582 100644 --- a/source/community.rst +++ b/source/community.rst @@ -1,12 +1,14 @@ Community ========= +.. include:: _old_docs_warning.rst + There are several ways to get in touch with the QIIME 2 community and stay up-to-date with QIIME 2 activity. QIIME 2 Forum ------------- -Visit the `QIIME 2 forum`_ for QIIME 2 support and to talk with other users and developers about all things related to QIIME 2. +Visit the QIIME 2 Forum for QIIME 2 support and to talk with other users and developers about all things related to QIIME 2. Staying updated --------------- @@ -19,5 +21,3 @@ Requesting features, reporting bugs, providing feedback If there is specific functionality you'd like to see in QIIME 2, you notice a bug, or want to leave feedback, please post to the `QIIME 2 forum`_. We appreciate all feedback as we strive to make QIIME 2 a useful and accessible tool for microbiome analyses. .. _`@qiime2`: https://twitter.com/qiime2 - -.. _`QIIME 2 forum`: https://forum.qiime2.org diff --git a/source/concepts.rst b/source/concepts.rst index 63a3d3cd..0096112a 100644 --- a/source/concepts.rst +++ b/source/concepts.rst @@ -1,6 +1,8 @@ Core concepts ============= +.. include:: _old_docs_warning.rst + This page describes several core concepts in QIIME 2 that are important to understand before starting to use the software. The :doc:`glossary ` may be helpful to refer to as you read through this page and other documentation on the site. Data files: QIIME 2 artifacts diff --git a/source/conf.py b/source/conf.py index 1954fcc5..9e76e31d 100644 --- a/source/conf.py +++ b/source/conf.py @@ -92,7 +92,7 @@ def setup(app): # General information about the project. project = 'QIIME 2' -copyright = '2016-2024, QIIME 2 development team' +copyright = '2016-2025, QIIME 2 development team' author = 'QIIME 2 development team' # The version info for the project you're documenting, acts as replacement for diff --git a/source/data-resources.rst b/source/data-resources.rst index b167a6af..e9822d9c 100644 --- a/source/data-resources.rst +++ b/source/data-resources.rst @@ -1,6 +1,8 @@ Data resources ============== +.. include:: _old_docs_warning.rst + Taxonomy classifiers for use with q2-feature-classifier ------------------------------------------------------- diff --git a/source/getting-started.rst b/source/getting-started.rst index 1e6c3b9e..631af313 100644 --- a/source/getting-started.rst +++ b/source/getting-started.rst @@ -1,6 +1,8 @@ Getting started =============== +.. include:: _old_docs_warning.rst + This guide will walk you through the steps necessary to understand, install, and use QIIME 2 for your own microbiome analyses: 1. Familiarize yourself with the :doc:`core concepts ` of QIIME 2 before starting to use the system. diff --git a/source/glossary.rst b/source/glossary.rst index 9dc17eec..9920dd67 100644 --- a/source/glossary.rst +++ b/source/glossary.rst @@ -1,6 +1,8 @@ User Glossary ============= +.. include:: _old_docs_warning.rst + There are two glossaries for QIIME 2: one geared toward users (this document), and another geared toward developers. You can find the `Developer Glossary here `_. @@ -145,18 +147,18 @@ and another geared toward developers. You can find the See :term:`visualization`. rarefy - A technique to remove uneven sampling depth by subsampling without + A technique to remove uneven sampling depth by subsampling without replacement so that all :term: `samples ` have the same sampling - depth. See `Schloss (2024) ` for additional information. - + depth. See `Schloss (2024) ` for additional information. + rarefaction - An iterative technique to minimize effects of controlling for uneven - sampling depth where a feature table is :term:`rarefied` - multiple times (typically 100 or 1000), and diversity + An iterative technique to minimize effects of controlling for uneven + sampling depth where a feature table is :term:`rarefied` + multiple times (typically 100 or 1000), and diversity metrics are applied to each rarefied table and subsequently used to - compute summary statistics. See `Schloss (2024) ` for additional information. - + compute summary statistics. See `Schloss (2024) ` for additional information. + result A general term for an :term:`artifact` or a :term:`visualization`. diff --git a/source/index.rst b/source/index.rst index de168cac..6fe6d4ca 100644 --- a/source/index.rst +++ b/source/index.rst @@ -1,12 +1,7 @@ -QIIME 2 user documentation -========================== +This is the "old" QIIME 2 user documentation +============================================ -This site is the official user documentation for QIIME™ 2, including installation instructions, tutorials, and other important information. Visit http://qiime.org for information on QIIME™ 1. - -Getting started ---------------- - -Check out the :doc:`getting started ` guide to begin using QIIME 2. +.. include:: _old_docs_warning.rst Table of contents ----------------- @@ -28,5 +23,3 @@ Table of contents supplementary-resources glossary citation - -.. _QIIME 1: http://qiime.org diff --git a/source/install/index.rst b/source/install/index.rst index 044aae4a..b71a043a 100644 --- a/source/install/index.rst +++ b/source/install/index.rst @@ -1,6 +1,8 @@ Installing QIIME 2 ================== +.. include:: ../_old_docs_warning.rst + QIIME 2 can be installed natively or using a virtual machine. The following pages describe how to install the available :ref:`distributions` in either scenario. diff --git a/source/install/native.rst b/source/install/native.rst index 899253f5..72b3b6e8 100644 --- a/source/install/native.rst +++ b/source/install/native.rst @@ -1,6 +1,8 @@ Natively installing QIIME 2 =========================== +.. include:: ../_old_docs_warning.rst + This guide describes how to natively install the available :ref:`distributions`. Miniconda diff --git a/source/install/virtual/docker.rst b/source/install/virtual/docker.rst index 5ad31970..9c0c7f5f 100644 --- a/source/install/virtual/docker.rst +++ b/source/install/virtual/docker.rst @@ -1,6 +1,8 @@ Installing QIIME 2 using Docker =============================== +.. include:: ../../_old_docs_warning.rst + The following QIIME 2 distributions are available as Docker images: - ``amplicon`` diff --git a/source/install/virtual/index.rst b/source/install/virtual/index.rst index 010d09b8..fb1eefbf 100644 --- a/source/install/virtual/index.rst +++ b/source/install/virtual/index.rst @@ -1,6 +1,8 @@ Installing QIIME 2 using a Virtual Machine ========================================== +.. include:: ../../_old_docs_warning.rst + *QIIME 2 Distribution* builds are available as Docker Images. See :ref:`distributions` for more details about the available distributions. .. toctree:: diff --git a/source/install/virtual/wsl.rst b/source/install/virtual/wsl.rst index 39c628e7..0b85fe94 100644 --- a/source/install/virtual/wsl.rst +++ b/source/install/virtual/wsl.rst @@ -1,6 +1,8 @@ Installing QIIME 2 using WSL ---------------------------- +.. include:: ../../_old_docs_warning.rst + Please see the `official Microsoft guide`_ to install and set up the WSL. Once you have installed and set up the WSL, install a Linux distribution (step 6 of the WSL guide). We suggest the latest stable version of `Ubuntu`_. @@ -14,4 +16,3 @@ setting up and using the WSL. .. _official Microsoft guide: https://docs.microsoft.com/en-us/windows/wsl/install-win10 .. _Ubuntu: https://wiki.ubuntu.com/WSL -.. _QIIME 2 Forum: https://forum.qiime2.org/search?q=WSL%20%23community-contributions diff --git a/source/interfaces/artifact-api.rst b/source/interfaces/artifact-api.rst index 0ded5529..609735b0 100644 --- a/source/interfaces/artifact-api.rst +++ b/source/interfaces/artifact-api.rst @@ -1,6 +1,8 @@ Artifact API (using QIIME 2 with Python) ======================================== +.. include:: ../_old_docs_warning.rst + .. note:: This guide assumes you have performed the steps in the :doc:`Moving Pictures tutorial <../tutorials/moving-pictures>`. The ``table.qza`` and ``sample-metadata.tsv`` files generated in that tutorial are used here. The Artifact API is a Python 3 application programming interface (API) for QIIME 2. The Artifact API supports interactive computing with QIIME 2 using the Python 3 programming language. This API is intended for advanced/technical users. The API is automatically generated, and its availability depends on which QIIME 2 plugins are currently installed. It has been optimized for use in the `Jupyter Notebook`_, which is currently our primary target for use of this API. The Artifact API is a part of the QIIME 2 framework; no additional software needs to be installed to use it. diff --git a/source/interfaces/index.rst b/source/interfaces/index.rst index e2660ff9..1fd2b7bb 100644 --- a/source/interfaces/index.rst +++ b/source/interfaces/index.rst @@ -1,6 +1,8 @@ Interfaces ========== +.. include:: ../_old_docs_warning.rst + .. toctree:: :maxdepth: 2 diff --git a/source/interfaces/q2cli.rst b/source/interfaces/q2cli.rst index d0e4ee27..0e3969f0 100644 --- a/source/interfaces/q2cli.rst +++ b/source/interfaces/q2cli.rst @@ -1,6 +1,8 @@ QIIME 2 command-line interface (q2cli) ====================================== +.. include:: ../_old_docs_warning.rst + .. note:: This guide assumes you have installed the QIIME 2 Amplicon distribution using one of the procedures in the :doc:`install documents <../install/index>`. This guide provides an introduction to ``q2cli``, a QIIME 2 command-line interface included in each of the available QIIME 2 distributions. The :doc:`tutorials <../tutorials/index>` use ``q2cli`` extensively, so it is recommended to review this document first before beginning the tutorials. This document is a work-in-progress and will be expanded in the future. diff --git a/source/jupyter-book-tutorials.rst b/source/jupyter-book-tutorials.rst index abbb523d..c861173c 100644 --- a/source/jupyter-book-tutorials.rst +++ b/source/jupyter-book-tutorials.rst @@ -1,6 +1,8 @@ Jupyter Book Tutorials ============================ +.. include:: _old_docs_warning.rst + These tutorials are powered by `Jupyter Book `_, a Jupyter-based documentation tool developed with support from the `Sloan Foundation `_. diff --git a/source/plugins/developing.rst b/source/plugins/developing.rst index 7e796bbe..9d216acb 100644 --- a/source/plugins/developing.rst +++ b/source/plugins/developing.rst @@ -1,7 +1,9 @@ Developing a QIIME 2 plugin =========================== -.. note:: This document is a work in progress, and serves as basic instructions for creating a QIIME 2 plugin. You can also find some (very preliminary) developer documentation at `https://dev.qiime2.org `__. +.. include:: ../_old_docs_warning.rst + +.. note:: This content is outdated. Instead, please refer to https://develop.qiime2.org. Creating a QIIME 2 plugin allows you to provide microbiome analysis functionality to QIIME 2 users. A plugin can be a standalone software project, or you can make a few small additions to your existing software project to make it a QIIME 2 plugin. Creating a single QIIME 2 plugin will make your functionality accessible through any QIIME 2 interface, including the :doc:`q2cli <../interfaces/q2cli>`, and the :doc:`Artifact API <../interfaces/artifact-api>`. diff --git a/source/plugins/future.rst b/source/plugins/future.rst index 33f540ba..eea3b883 100644 --- a/source/plugins/future.rst +++ b/source/plugins/future.rst @@ -1,9 +1,10 @@ Future plugins ============== +.. include:: ../_old_docs_warning.rst + Plugins planned for future releases and non-core plugins are discussed in the `QIIME 2 Forum`_. If you have questions about the availability of QIIME 2 methods, actions, pipelines, or plugins, please post your questions there. If you are working on a plugin that is not part of an existing QIIME 2 distribution, but you'd like to inform QIIME 2 users about it, you should post a topic to the `Community Plugins category`_ on the forum. If you're looking for documentation on how to develop a plugin, see :doc:`this guide `. -.. _QIIME 2 Forum: https://forum.qiime2.org .. _Community Plugins category: https://forum.qiime2.org/c/community-plugins diff --git a/source/plugins/index.rst b/source/plugins/index.rst index e2b512e0..d1daeb9f 100644 --- a/source/plugins/index.rst +++ b/source/plugins/index.rst @@ -1,6 +1,8 @@ Plugins ======= +.. include:: ../_old_docs_warning.rst + The following pages describe what QIIME 2 plugins are available and how to develop a new plugin. .. toctree:: diff --git a/source/semantic-types.rst b/source/semantic-types.rst index 384230a7..bca5bc99 100644 --- a/source/semantic-types.rst +++ b/source/semantic-types.rst @@ -1,6 +1,8 @@ Semantic types ============== +.. include:: _old_docs_warning.rst + All QIIME 2 artifacts have defined semantic types. This document is a placeholder for full documentation of how to use these types and how to define new semantic types in QIIME 2 plugins. Why define semantic types? diff --git a/source/supplementary-resources.rst b/source/supplementary-resources.rst index 8612d604..8e4e76f0 100644 --- a/source/supplementary-resources.rst +++ b/source/supplementary-resources.rst @@ -1,6 +1,8 @@ Supplementary resources ======================= +.. include:: _old_docs_warning.rst + Educational content ------------------- diff --git a/source/tutorials/atacama-soils.rst b/source/tutorials/atacama-soils.rst index 3ad7aad3..15aacb6a 100644 --- a/source/tutorials/atacama-soils.rst +++ b/source/tutorials/atacama-soils.rst @@ -1,6 +1,8 @@ "Atacama soil microbiome" tutorial ================================== +.. include:: ../_old_docs_warning.rst + .. note:: This guide assumes you have installed QIIME 2 using one of the procedures in the :doc:`install documents <../install/index>` and completed the :doc:`moving pictures tutorial `. diff --git a/source/tutorials/chimera.rst b/source/tutorials/chimera.rst index 8563267c..1ca479ee 100644 --- a/source/tutorials/chimera.rst +++ b/source/tutorials/chimera.rst @@ -1,6 +1,8 @@ Identifying and filtering chimeric feature sequences with q2-vsearch ==================================================================== +.. include:: ../_old_docs_warning.rst + Chimera checking in QIIME 2 is performed on a pair of ``FeatureTable[Frequency]`` and ``FeatureData[Sequences]`` artifacts. QIIME 2 wraps the Uchime *de novo* and reference pipelines from vsearch. For details on how these work, see the original `Uchime paper`_, and the `vsearch`_ documentation. In this tutorial, we'll use the table and sequences from the :doc:`Atacama soils tutorial `. diff --git a/source/tutorials/exporting.rst b/source/tutorials/exporting.rst index adebf9db..7d8278ca 100644 --- a/source/tutorials/exporting.rst +++ b/source/tutorials/exporting.rst @@ -1,6 +1,8 @@ Exporting data ============== +.. include:: ../_old_docs_warning.rst + .. note:: This tutorial assumes you have installed QIIME 2 using one of the procedures in the :doc:`install documents <../install/index>`. In order to use QIIME 2, your input data must be stored in *QIIME 2 artifacts* (i.e. ``.qza`` files). This is what enables distributed and automatic provenance tracking, as well as semantic type validation and transformations between data formats (see the :doc:`core concepts <../concepts>` page for more details about QIIME 2 artifacts). diff --git a/source/tutorials/feature-classifier.rst b/source/tutorials/feature-classifier.rst index c6ea58ed..664ace13 100644 --- a/source/tutorials/feature-classifier.rst +++ b/source/tutorials/feature-classifier.rst @@ -1,6 +1,8 @@ Training feature classifiers with q2-feature-classifier ======================================================= +.. include:: ../_old_docs_warning.rst + .. note:: This guide assumes you have installed QIIME 2 using one of the procedures in the :doc:`install documents <../install/index>`. This tutorial will demonstrate how to train ``q2-feature-classifier`` for a particular dataset. We will train the `Naive Bayes`_ classifier using `Greengenes`_ reference sequences and classify the representative sequences from the `Moving Pictures`_ dataset. @@ -111,7 +113,6 @@ In our experience, fungal ITS classifiers trained on the `UNITE reference databa .. _Moving Pictures: ../moving-pictures/index.html -.. _QIIME 2 forum: https://forum.qiime2.org/c/community-contributions/data-resources .. _Naive Bayes: http://scikit-learn.org/stable/modules/naive_bayes.html#multinomial-naive-bayes .. _Greengenes: http://qiime.org/home_static/dataFiles.html .. _(Werner et al., 2012): https://www.ncbi.nlm.nih.gov/pubmed/21716311 diff --git a/source/tutorials/filtering.rst b/source/tutorials/filtering.rst index 508f794b..92e07b9e 100644 --- a/source/tutorials/filtering.rst +++ b/source/tutorials/filtering.rst @@ -1,6 +1,8 @@ Filtering data ============== +.. include:: ../_old_docs_warning.rst + .. note:: This guide assumes you have installed QIIME 2 using one of the procedures in the :doc:`install documents <../install/index>`. This tutorial describes how to filter feature tables, sequences, and distance matrices in QIIME 2, and will be expanded as more filtering functionality becomes available. diff --git a/source/tutorials/fmt.rst b/source/tutorials/fmt.rst index 345a6552..f021b10b 100644 --- a/source/tutorials/fmt.rst +++ b/source/tutorials/fmt.rst @@ -1,6 +1,8 @@ Fecal microbiota transplant (FMT) study: an exercise ==================================================== +.. include:: ../_old_docs_warning.rst + .. note:: This guide assumes you have installed QIIME 2 using one of the procedures in the :doc:`install guides <../install/index>`. This document is intended to be run after :doc:`the moving pictures tutorial `. It is designed to introduce a few new ideas, and to be an exercise in applying the tools that were explored in that document. diff --git a/source/tutorials/importing.rst b/source/tutorials/importing.rst index be7f3d87..633e617f 100644 --- a/source/tutorials/importing.rst +++ b/source/tutorials/importing.rst @@ -1,6 +1,8 @@ Importing data ============== +.. include:: ../_old_docs_warning.rst + .. contents:: Importing data :depth: 2 @@ -541,7 +543,6 @@ If you have any questions, please post to the `QIIME 2 Forum`_ for help! .. _Earth Microbiome Project (EMP) protocol: http://www.earthmicrobiome.org/protocols-and-standards/ -.. _QIIME 2 Forum: https://forum.qiime2.org .. _BIOM v1.0.0 format specification: http://biom-format.org/documentation/format_versions/biom-1.0.html diff --git a/source/tutorials/index.rst b/source/tutorials/index.rst index 3c77aed5..f55af493 100644 --- a/source/tutorials/index.rst +++ b/source/tutorials/index.rst @@ -1,6 +1,8 @@ Tutorials ========= +.. include:: ../_old_docs_warning.rst + .. note:: The tutorials assume you have installed the QIIME 2 Amplicon Distribution using one of the procedures in the :doc:`install documents <../install/index>`. The tutorials make extensive use of the QIIME 2 command-line interface so reviewing the :doc:`q2cli docs <../interfaces/q2cli>` is recommended. .. toctree:: diff --git a/source/tutorials/longitudinal.rst b/source/tutorials/longitudinal.rst index 2cbcfffc..4a258551 100644 --- a/source/tutorials/longitudinal.rst +++ b/source/tutorials/longitudinal.rst @@ -1,6 +1,8 @@ Performing longitudinal and paired sample comparisons with q2-longitudinal ========================================================================== +.. include:: ../_old_docs_warning.rst + .. note:: This guide assumes you have installed QIIME 2 using one of the procedures in the :doc:`install documents <../install/index>`. This tutorial will demonstrate the various features of ``q2-longitudinal``, a plugin that supports statistical and visual comparisons of longitudinal study designs and paired samples, to determine if/how samples change between observational "states". "States" will most commonly be related to time or an environmental gradient, and for paired analyses (``pairwise-distances`` and ``pairwise-differences``) the sample pairs should typically consist of the same individual subject observed at two different time points. For example, patients in a clinical study whose stool samples are collected before and after receiving treatment. diff --git a/source/tutorials/metadata.rst b/source/tutorials/metadata.rst index 4af9f3f1..88d0212b 100644 --- a/source/tutorials/metadata.rst +++ b/source/tutorials/metadata.rst @@ -1,6 +1,8 @@ Metadata in QIIME 2 =================== +.. include:: ../_old_docs_warning.rst + .. note:: This guide assumes you have installed QIIME 2 using one of the procedures in the :doc:`install documents <../install/index>` and completed the :doc:`moving pictures tutorial `. Metadata provides the key to gaining biological insight from your data. In QIIME 2, *sample metadata* may include technical details, such as the DNA barcodes that were used for each sample in a multiplexed sequencing run, or descriptions of the samples, such as which subject, time point, and body site each sample came from in a human microbiome time series. *Feature metadata* is often a feature annotation, such as the taxonomy assigned to a sequence variant or OTU. Sample and feature metadata are used by many plugins in QIIME 2, and examples are provided in this tutorial (and other QIIME 2 tutorials) illustrating how to use metadata in your own microbiome analyses. diff --git a/source/tutorials/moving-pictures-usage.rst b/source/tutorials/moving-pictures-usage.rst index 1ad2d00f..0e5f6c8f 100644 --- a/source/tutorials/moving-pictures-usage.rst +++ b/source/tutorials/moving-pictures-usage.rst @@ -1,6 +1,8 @@ "Moving Pictures" tutorial - Multiple Interface Edition ======================================================= +.. include:: ../_old_docs_warning.rst + Beta preview note ----------------- diff --git a/source/tutorials/moving-pictures.rst b/source/tutorials/moving-pictures.rst index 37a37fc2..d5f4e51d 100644 --- a/source/tutorials/moving-pictures.rst +++ b/source/tutorials/moving-pictures.rst @@ -1,6 +1,8 @@ "Moving Pictures" tutorial ========================== +.. include:: ../_old_docs_warning.rst + .. note:: This guide assumes you have installed QIIME 2 using one of the procedures in the :doc:`install documents <../install/index>`. .. note:: This guide uses QIIME 2-specific terminology, please see the :doc:`glossary <../glossary>` for more details. diff --git a/source/tutorials/otu-clustering.rst b/source/tutorials/otu-clustering.rst index 1d728355..e8a0ac96 100644 --- a/source/tutorials/otu-clustering.rst +++ b/source/tutorials/otu-clustering.rst @@ -1,6 +1,8 @@ Clustering sequences into OTUs using q2-vsearch =============================================== +.. include:: ../_old_docs_warning.rst + *De novo*, closed-reference, and open-reference clustering are currently supported in QIIME 2. diff --git a/source/tutorials/overview.rst b/source/tutorials/overview.rst index b3a8b45f..1471787f 100644 --- a/source/tutorials/overview.rst +++ b/source/tutorials/overview.rst @@ -1,6 +1,8 @@ Overview of QIIME 2 Plugin Workflows ==================================== +.. include:: ../_old_docs_warning.rst + .. note:: Abandon all hope, ye who enter, if you have not read the :doc:`glossary <../glossary>`. 👺 .. note:: This is a guide for novice QIIME 2 users, and particularly for those who are new to microbiome research. For experienced users who are already well versed in microbiome analysis, and those who are averse to uncontrolled use of emoji, mosey on over to the :doc:`overview tutorial for experienced users `. diff --git a/source/tutorials/pd-mice.rst b/source/tutorials/pd-mice.rst index ff6ad8e9..7b7a9edf 100644 --- a/source/tutorials/pd-mice.rst +++ b/source/tutorials/pd-mice.rst @@ -1,6 +1,8 @@ Parkinson's Mouse Tutorial -------------------------- +.. include:: ../_old_docs_warning.rst + This tutorial will demonstrate a "typical" QIIME 2 analysis of 16S rRNA gene amplicon data, using a set of fecal samples from `humanized`_ mice. The original study, `Sampson et al, 2016`_, was designed to determine whether the fecal microbiome contributed to the development of Parkinson's Disease (PD). Several observation studies showed a difference in the microbiome between PD patients and controls, although the organisms identified across studies were not consistent. However, this was sufficient evidence to suggest that there might be a relationship between PD and the fecal microbiome. To determine whether that relationship was incidental or actually disease associated, a second study was needed. A human cohort study was not feasible; the disease only affects about 1% of the population over 60 years old, PD takes a long time to develop and to be diagnosed, and it would be difficult to determine when to collect the samples. Therefore, a gnotobiotic mouse study was utilized to evaluate the role of the microbiome in the development of PD symptoms. Feces were collected from six donors with Parkinson's disease and six age- and sex-matched neurologically healthy controls, and then transplanted into mice who were either predisposed to developing Parkinson's disease due to a mutation ("aSyn") or resistant wild type mice ("BDF1"). Mice from different donors were kept in separate cages, but mice from different genetic backgrounds were co-housed. The mice were followed for 7 weeks to see if they developed symptoms of Parkinson's disease. diff --git a/source/tutorials/phylogeny.rst b/source/tutorials/phylogeny.rst index fefe5171..6b6afaed 100644 --- a/source/tutorials/phylogeny.rst +++ b/source/tutorials/phylogeny.rst @@ -1,6 +1,8 @@ Phylogenetic inference with q2-phylogeny ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.. include:: ../_old_docs_warning.rst + .. contents:: Phylogenetic inference with q2-phylogeny :depth: 4 diff --git a/source/tutorials/qiime2-for-experienced-microbiome-researchers.rst b/source/tutorials/qiime2-for-experienced-microbiome-researchers.rst index 418ef551..8b7f61ee 100644 --- a/source/tutorials/qiime2-for-experienced-microbiome-researchers.rst +++ b/source/tutorials/qiime2-for-experienced-microbiome-researchers.rst @@ -1,6 +1,7 @@ QIIME 2 for Experienced Microbiome Researchers ############################################## +.. include:: ../_old_docs_warning.rst .. contents:: QIIME 2 for Experienced Microbiome Researchers :depth: 3 diff --git a/source/tutorials/quality-control.rst b/source/tutorials/quality-control.rst index 2da5633f..25ebdda1 100644 --- a/source/tutorials/quality-control.rst +++ b/source/tutorials/quality-control.rst @@ -1,6 +1,8 @@ Evaluating and controlling data quality with q2-quality-control =============================================================== +.. include:: ../_old_docs_warning.rst + .. note:: This guide assumes you have installed QIIME 2 using one of the procedures in the :doc:`install documents <../install/index>` and completed the :doc:`moving pictures tutorial `. This tutorial will demonstrate how to use the ``q2-quality-control`` plugin to evaluate data quality based on mock communities (or other samples with known compositions) and filter sequence data. diff --git a/source/tutorials/read-joining.rst b/source/tutorials/read-joining.rst index b8cb4782..a1060db2 100644 --- a/source/tutorials/read-joining.rst +++ b/source/tutorials/read-joining.rst @@ -1,6 +1,8 @@ Alternative methods of read-joining in QIIME 2 ============================================== +.. include:: ../_old_docs_warning.rst + .. note:: This tutorial does not cover read-joining and denoising with DADA2. Instead, this tutorial focuses on alternative approaches to analyzing paired-end reads in QIIME 2. If you are interested in joining and denoising diff --git a/source/tutorials/sample-classifier.rst b/source/tutorials/sample-classifier.rst index 62624c85..760b842a 100644 --- a/source/tutorials/sample-classifier.rst +++ b/source/tutorials/sample-classifier.rst @@ -1,6 +1,8 @@ Predicting sample metadata values with q2-sample-classifier =========================================================== +.. include:: ../_old_docs_warning.rst + .. note:: Documentation for using all plugin actions through the Python API and command line interface is available in the q2-sample-classifier :doc:`reference documentation <../plugins/available/sample-classifier/index>`. .. note:: This guide assumes you have installed QIIME 2 using one of the procedures in the :doc:`install documents <../install/index>` and completed the :doc:`moving pictures tutorial `. diff --git a/source/tutorials/utilities.rst b/source/tutorials/utilities.rst index e183e7c7..9b4b2001 100644 --- a/source/tutorials/utilities.rst +++ b/source/tutorials/utilities.rst @@ -1,6 +1,8 @@ Utilities in QIIME 2 ==================== +.. include:: ../_old_docs_warning.rst + .. contents:: :depth: 3