Welcome to dokdo’s documentation!

Contents:

• README
  • Introduction
  • Citation
  • Support Dokdo
  • CLI Examples
  • API Examples
  • Getting Started
  • Package Purpose
• Dokdo CLI
  • Introduction
  • Commands
• Dokdo API
  • Introduction
  • General Methods
  • Main Plotting Methods
  • Other Plotting Methods
• QIIME 2 CLI
  • Introduction
  • Removal of Adapters and Primers
  • Import Sequences to QIIME 2
  • Identify ASVs
  • Merge Multiple Sequencing Runs
  • Alpha Rarefaction
  • Beta Rarefaction
  • Compute Core Metrics
  • Alpha Diversity Significance
  • Beta Diversity Significance
  • Build Phylogenetic Tree
  • Filtering Data
  • Taxonomy Classifier
  • Classify Taxonomy
  • Create Taxonomy Barplot
  • Differential Abundance
  • Taxonomy to Sequence
  • Exporting Artifacts
  • Biplot
• QIIME 2 API
  • Introduction
  • Get Sample IDs from Metadata
  • Filter Samples from ASV Table
  • Rarefy ASV Table
  • Compute Distance Matrix
  • Visualize Ordination
  • Alpha Rarefaction
  • Collapse Feature Table
• Useful Information
  • Introduction
  • Adapters and Primers
  • Alpha Diversity
  • Beta Diversity
  • ASV Identification by DADA2
  • Differential Abundance
  • Common Contaminants and Negative Controls
  • Meaning of Double Underscore in Taxa Names
  • Beta Significance Test
  • RuntimeError by Click in Non-US Server
  • phyloseq
  • decontam
• Pipeline
  • Introduction
  • Directory Structure
  • 1. Demultiplexing
  • 2. Import Sequences to QIIME 2
  • 3. Identify ASVs
  • 4. Merge Multiple Sequencing Runs
  • 5. Classify Taxonomy
  • 6. Summarize and Filter ASV Table
  • 7. Build Phylogenetic Tree
  • 8. Create Rarefaction Curves
  • 9. Compute Core Metrics
  • 10. Create Taxonomy Barplot
• Changelog
  • 1.16.0 (2022-12-27)
  • 1.15.0 (2022-08-23)
  • 1.14.0 (2022-06-24)
  • 1.13.0 (2022-04-02)
  • 1.12.0 (2022-02-11)
  • 1.11.0 (2021-08-04)
  • 1.10.0 (2021-07-06)
  • 1.9.0 (2021-06-07)
  • 1.8.0 (2021-05-09)
  • 1.7.0 (2021-04-05)
  • 1.6.0 (2021-03-08)
  • 1.5.0 (2021-02-03)
  • 1.4.0 (2021-01-09)
  • 1.3.0 (2020-12-23)
  • 1.2.0 (2020-12-08)
  • 1.1.0 (2020-11-23)
  • 1.0.0 (2020-11-09)

Indices and tables

• Index

• Module Index

• Search Page