QIIME 2

https://docs.qiime2.org/2024.10/
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QIIME 2 is a microbiome bioinformatics platform for analyzing marker gene and metagenomic sequencing...
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### Command line interface examples for tabulate-seqs

Source: https://docs.qiime2.org/2024.10/plugins/available/feature-table/tabulate-seqs

Examples demonstrating how to use the tabulate-seqs command with different input configurations.

```bash
qiime feature-table tabulate-seqs \
  --i-data rep-seqs.qza \
  --o-visualization rep-seqs.qzv
```

```bash
qiime feature-table tabulate-seqs \
  --i-data rep-seqs-single-taxon.qza \
  --i-taxonomy single-taxonomy.qza \
  --o-visualization rep-seqs.qzv
```

```bash
qiime feature-table tabulate-seqs \
  --i-data rep-seqs-multi-taxon.qza \
  --i-taxonomy multi-taxonomy/ \
  --o-visualization rep-seqs.qzv
```

--------------------------------

### Command Line Interface Examples

Source: https://docs.qiime2.org/2024.10/plugins/available/stats/mann-whitney-u-facet

Examples for running the mann-whitney-u-facet action via the QIIME 2 CLI with different faceting options.

```bash
qiime stats mann-whitney-u-facet \
  --i-distribution dist.qza \
  --p-facet across \
  --o-stats stats.qza
```

```bash
qiime stats mann-whitney-u-facet \
  --i-distribution dist.qza \
  --p-facet within \
  --o-stats stats.qza
```

--------------------------------

### Install QIIME 2 Tiny on Linux and Windows (WSL)

Source: https://docs.qiime2.org/2024.10/install/native

Standard installation command for Linux environments and Windows Subsystem for Linux.

```bash
conda env create -n qiime2-tiny-2024.10 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py310-linux-conda.yml
```

--------------------------------

### Download Example FASTA Data

Source: https://docs.qiime2.org/2024.10/tutorials/importing

Commands to download the example sequences.fna file using wget or curl.

```bash
wget \
  -O "sequences.fna" \
  "https://data.qiime2.org/2024.10/tutorials/importing/sequences.fna"
```

```bash
curl -sL \
  "https://data.qiime2.org/2024.10/tutorials/importing/sequences.fna" > \
  "sequences.fna"
```

--------------------------------

### Command Line Interface Example

Source: https://docs.qiime2.org/2024.10/plugins/available/diversity/alpha-correlation

Example usage of the alpha-correlation command to analyze Faith PD diversity against sample metadata.

```bash
qiime diversity alpha-correlation \
  --i-alpha-diversity alpha-div-faith-pd.qza \
  --m-metadata-file metadata.tsv \
  --o-visualization visualization.qzv
```

--------------------------------

### Display deployment information

Source: https://docs.qiime2.org/2024.10/interfaces/q2cli

Use the info subcommand to list installed plugins and deployment details.

```bash
qiime info
```

--------------------------------

### Manifest file content

Source: https://docs.qiime2.org/2024.10/tutorials/pd-mice

Example of the expected tab-separated format for the sample manifest file.

```text
sample-id	absolute-filepath
recip.220.WT.OB1.D7	$PWD/demultiplexed_seqs/10483.recip.220.WT.OB1.D7_30_L001_R1_001.fastq.gz
recip.290.ASO.OB2.D1	$PWD/demultiplexed_seqs/10483.recip.290.ASO.OB2.D1_27_L001_R1_001.fastq.gz
recip.389.WT.HC2.D21	$PWD/demultiplexed_seqs/10483.recip.389.WT.HC2.D21_1_L001_R1_001.fastq.gz
recip.391.ASO.PD2.D14	$PWD/demultiplexed_seqs/10483.recip.391.ASO.PD2.D14_5_L001_R1_001.fastq.gz
recip.391.ASO.PD2.D21	$PWD/demultiplexed_seqs/10483.recip.391.ASO.PD2.D21_1_L001_R1_001.fastq.gz
recip.391.ASO.PD2.D7	$PWD/demultiplexed_seqs/10483.recip.391.ASO.PD2.D7_15_L001_R1_001.fastq.gz
recip.400.ASO.HC2.D14	$PWD/demultiplexed_seqs/10483.recip.400.ASO.HC2.D14_32_L001_R1_001.fastq.gz
recip.401.ASO.HC2.D7	$PWD/demultiplexed_seqs/10483.recip.401.ASO.HC2.D7_22_L001_R1_001.fastq.gz
recip.403.ASO.PD2.D21	$PWD/demultiplexed_seqs/10483.recip.403.ASO.PD2.D21_31_L001_R1_001.fastq.gz
```

--------------------------------

### Download and Extract Example Data

Source: https://docs.qiime2.org/2024.10/tutorials/importing

Commands to download the Casava 1.8 example dataset using wget or curl, followed by extraction.

```bash
wget \
  -O "casava-18-paired-end-demultiplexed.zip" \
  "https://data.qiime2.org/2024.10/tutorials/importing/casava-18-paired-end-demultiplexed.zip"
```

```bash
curl -sL \
  "https://data.qiime2.org/2024.10/tutorials/importing/casava-18-paired-end-demultiplexed.zip" > \
  "casava-18-paired-end-demultiplexed.zip"
```

```bash
unzip -q casava-18-paired-end-demultiplexed.zip
```

--------------------------------

### Verify QIIME 2 Installation

Source: https://docs.qiime2.org/2024.10/install/native

Runs the help command to ensure the environment is correctly configured and functional.

```bash
qiime --help
```

--------------------------------

### Create Fastq Manifest Files

Source: https://docs.qiime2.org/2024.10/tutorials/importing

Examples of tab-separated manifest files mapping sample IDs to absolute filepaths for paired-end and single-end data.

```text
sample-id     forward-absolute-filepath       reverse-absolute-filepath
sample-1      $PWD/some/filepath/sample0_R1.fastq.gz  $PWD/some/filepath/sample1_R2.fastq.gz
sample-2      $PWD/some/filepath/sample2_R1.fastq.gz  $PWD/some/filepath/sample2_R2.fastq.gz
sample-3      $PWD/some/filepath/sample3_R1.fastq.gz  $PWD/some/filepath/sample3_R2.fastq.gz
sample-4      $PWD/some/filepath/sample4_R1.fastq.gz  $PWD/some/filepath/sample4_R2.fastq.gz
```

```text
sample-id     absolute-filepath
sample-1      $PWD/some/filepath/sample1_R1.fastq
sample-2      $PWD/some/filepath/sample2_R1.fastq
```

--------------------------------

### Install QIIME 2 Tiny on macOS (Apple Silicon)

Source: https://docs.qiime2.org/2024.10/install/native

Configures the installation in Rosetta 2 emulation mode for Apple Silicon chips.

```bash
CONDA_SUBDIR=osx-64 conda env create -n qiime2-tiny-2024.10 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py310-osx-conda.yml
conda activate qiime2-tiny-2024.10
conda config --env --set subdir osx-64
```

--------------------------------

### Run beta-passthrough via Command Line Interface

Source: https://docs.qiime2.org/2024.10/plugins/available/diversity-lib/beta-passthrough

Examples of executing the beta-passthrough command with different configurations for core usage, metrics, and pseudocounts.

```bash
qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --o-distance-matrix euclidean-dm.qza
```

```bash
qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric euclidean \
  --p-n-jobs 1 \
  --o-distance-matrix euclidean-dm.qza
```

```bash
qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --o-distance-matrix aitchison-dm.qza
```

```bash
qiime diversity-lib beta-passthrough \
  --i-table feature-table.qza \
  --p-metric aitchison \
  --p-n-jobs auto \
  --p-pseudocount 5 \
  --o-distance-matrix aitchison-dm.qza
```

--------------------------------

### Download example data

Source: https://docs.qiime2.org/2024.10/tutorials/importing

Use wget or curl to retrieve the unrooted tree file from the QIIME 2 data repository.

```bash
wget \
  -O "unrooted-tree.tre" \
  "https://data.qiime2.org/2024.10/tutorials/importing/unrooted-tree.tre"
```

```bash
curl -sL \
  "https://data.qiime2.org/2024.10/tutorials/importing/unrooted-tree.tre" > \
  "unrooted-tree.tre"
```

--------------------------------

### IQ-TREE execution output

Source: https://docs.qiime2.org/2024.10/tutorials/phylogeny

Example of the standard output generated by the iqtree command, showing internal configuration and alignment analysis.

```text
IQ-TREE multicore version 2.3.6 for MacOS Intel 64-bit built Aug  4 2024
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt,
Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong

Host:    88.local (SSE4.2, 18 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/1t/w4ys4pks4q5d5_kl7svl4t080000gn/T/qiime2/jgc/data/d34420d9-336e-4d9e-aee8-99e64b3315f0/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/1t/w4ys4pks4q5d5_kl7svl4t080000gn/T/tmpb_3um885/q2iqtree -nt 1
Seed:    378176 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Thu Apr 24 17:23:43 2025
Kernel:  SSE2 - 1 threads (12 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 12 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading alignment file /var/folders/1t/w4ys4pks4q5d5_kl7svl4t080000gn/T/qiime2/jgc/data/d34420d9-336e-4d9e-aee8-99e64b3315f0/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 9.10759e-05 secs using 85.64% CPU
Alignment most likely contains DNA/RNA sequences
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
                                          Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 8.10623e-06 secs using 74.02% CPU
   1  e84fcf85a6a4065231dcf343bb862f1cb32abae6   40.65%    passed     90.91%
   2  5525fb6dab7b6577960147574465990c6df070ad   42.99%    passed     99.80%
   3  eb3564a35320b53cef22a77288838c7446357327   42.99%    passed     25.49%
   4  418f1d469f08c99976b313028cf6d3f18f61dd55   43.93%    passed     71.86%
   5  2e3b2c075901640c4de739473f9246385430b1ed   31.31%    passed     90.76%
   6  0469f8d819bd45c7638d1c8b0895270a05f34267   38.79%    passed     92.82%
   7  d162ed685007f5adede58f14aece31dfa1b60c18   40.65%    passed     97.17%
   8  1d45b2bce36cd995c5dcb755babf512e612ce8b9   41.59%    passed     39.04%
   9  5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8   31.31%    passed     87.21%
  10  206656bec2abdbc4aee37a661ef5f4a62b5dd6ae   42.99%    passed     85.00%
  11  606c23e79bb730ad74e3c6efd72004c36674c17a   47.20%    passed     87.78%
  12  682e91d7e510ab134d0625234ad224f647c14eb0   41.59%    passed     31.01%
  13  6a36152105590b1eb095b9503e8f1f226fc73e43   39.25%    passed     86.29%
  14  6ca685c39a33bfbcb3123129e7af88d573df7d6f   42.06%    failed      0.02%
  15  8a1c44eb462ed58b21f3fdd72dd22bb657db2980   31.78%    passed     54.40%
  16  9b220cae8d375ea38b8b481cb95949cda8722fcb   36.92%    passed     88.78%
  17  aa4698d2e2b1fa71d08e2934a923aad7374a18f6   37.85%    passed     90.52%
  18  b31aa3f04bc9d5e2498d45cf1983dfaf09faa258   31.78%    passed     72.69%
  19  d44b129a6181f052198bda3813f0802a91612441   41.59%    passed     41.69%
  20  ed1acad8a98e8579a44370733533ad7d3fed8006   48.13%    passed     58.15%
****  TOTAL                                      39.77%  1 sequences failed composition chi2 test (p-value<5%; df=3)

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
```

--------------------------------

### Install QIIME 2 Tiny on macOS (Intel)

Source: https://docs.qiime2.org/2024.10/install/native

Use this command for standard macOS Intel-based systems.

```bash
conda env create -n qiime2-tiny-2024.10 --file https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.10-py310-osx-conda.yml
```

--------------------------------

### Confirm QIIME 2 Installation

Source: https://docs.qiime2.org/2024.10/install/virtual/docker

Verify the image by running the qiime command within a container, mounting the current directory to /data.

```bash
docker run -t -i -v $(pwd):/data quay.io/qiime2/<distribution>:2024.10 qiime
```

--------------------------------

### Compute Shannon's Entropy via CLI

Source: https://docs.qiime2.org/2024.10/plugins/available/diversity-lib/shannon-entropy

Examples for running the shannon-entropy command, including basic usage and handling of undefined samples.

```bash
qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --o-vector shannon-vector.qza
```

```bash
qiime diversity-lib shannon-entropy \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector shannon-vector.qza
```

--------------------------------

### Compute Pielou's Evenness via CLI

Source: https://docs.qiime2.org/2024.10/plugins/available/diversity-lib/pielou-evenness

Examples for running the Pielou's Evenness calculation using the QIIME 2 command-line interface.

```bash
qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --o-vector pielou-vector.qza
```

```bash
qiime diversity-lib pielou-evenness \
  --i-table feature-table.qza \
  --p-drop-undefined-samples \
  --o-vector pielou-vector.qza
```

--------------------------------

### Create and enter tutorial directory

Source: https://docs.qiime2.org/2024.10/tutorials/moving-pictures/index.html

Initializes a new directory for the tutorial files and navigates into it.

```bash
mkdir qiime2-moving-pictures-tutorial
cd qiime2-moving-pictures-tutorial
```

--------------------------------

### Create and enter tutorial directory

Source: https://docs.qiime2.org/2024.10/tutorials/longitudinal

Initialize a new directory for the longitudinal tutorial files.

```bash
mkdir longitudinal-tutorial
cd longitudinal-tutorial
```

--------------------------------

### Create and enter working directory

Source: https://docs.qiime2.org/2024.10/tutorials/chimera

Initializes a new directory for the tutorial files.

```bash
mkdir qiime2-chimera-filtering-tutorial
cd qiime2-chimera-filtering-tutorial
```

--------------------------------

### Create directory for metadata tutorial

Source: https://docs.qiime2.org/2024.10/tutorials/metadata

Initialize a local directory to store tutorial files.

```bash
mkdir qiime2-metadata-tutorial
cd qiime2-metadata-tutorial
```

--------------------------------

### Create working directory

Source: https://docs.qiime2.org/2024.10/tutorials/otu-clustering

Initialize a new directory for the tutorial files.

```bash
mkdir qiime2-otu-clustering-tutorial
cd qiime2-otu-clustering-tutorial
```

--------------------------------

### Create working directory for sample-classifier tutorial

Source: https://docs.qiime2.org/2024.10/tutorials/sample-classifier

Initializes a new directory for the tutorial files and navigates into it.

```bash
mkdir sample-classifier-tutorial
cd sample-classifier-tutorial
```

--------------------------------

### Install QIIME 2 Pathogenome Distribution

Source: https://docs.qiime2.org/2024.10/install/native

Commands to install the Pathogenome distribution on various platforms, including Rosetta 2 emulation for Apple Silicon.

```bash
conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-osx-conda.yml
```

```bash
CONDA_SUBDIR=osx-64 conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-osx-conda.yml
conda activate qiime2-pathogenome-2024.10
conda config --env --set subdir osx-64
```

```bash
conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-linux-conda.yml
```

```bash
conda env create -n qiime2-pathogenome-2024.10 --file https://data.qiime2.org/distro/pathogenome/qiime2-pathogenome-2024.10-py310-linux-conda.yml
```

--------------------------------

### Create working directory

Source: https://docs.qiime2.org/2024.10/tutorials/fmt

Initialize the project environment by creating and entering a new directory.

```bash
mkdir qiime2-fmt-tutorial
cd qiime2-fmt-tutorial
```

--------------------------------

### Install QIIME 2 Metagenome Distribution

Source: https://docs.qiime2.org/2024.10/install/native

Commands to install the Metagenome distribution on various platforms, including Rosetta 2 emulation for Apple Silicon.

```bash
conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-osx-conda.yml
```

```bash
CONDA_SUBDIR=osx-64 conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-osx-conda.yml
conda activate qiime2-metagenome-2024.10
conda config --env --set subdir osx-64
```

```bash
conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-linux-conda.yml
```

```bash
conda env create -n qiime2-metagenome-2024.10 --file https://data.qiime2.org/distro/metagenome/qiime2-metagenome-2024.10-py310-linux-conda.yml
```

--------------------------------

### Install QIIME 2 Amplicon Distribution

Source: https://docs.qiime2.org/2024.10/install/native

Commands to install the Amplicon distribution on various platforms, including Rosetta 2 emulation for Apple Silicon.

```bash
conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-osx-conda.yml
```

```bash
CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-osx-conda.yml
conda activate qiime2-amplicon-2024.10
conda config --env --set subdir osx-64
```

```bash
conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml
```

```bash
conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml
```

--------------------------------

### IQ-TREE stdout output

Source: https://docs.qiime2.org/2024.10/tutorials/phylogeny

Example output generated by the IQ-TREE tool during execution.

```text
IQ-TREE multicore version 2.3.6 for MacOS Intel 64-bit built Aug  4 2024
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt,
Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong

Host:    88.local (SSE4.2, 18 GB RAM)
Command: iqtree -st DNA --runs 1 -s /var/folders/1t/w4ys4pks4q5d5_kl7svl4t080000gn/T/qiime2/jgc/data/d34420d9-336e-4d9e-aee8-99e64b3315f0/data/aligned-dna-sequences.fasta -m GTR+I+G -pre /var/folders/1t/w4ys4pks4q5d5_kl7svl4t080000gn/T/tmpfrpo28h5/q2iqtree -nt 1 -alrt 1000 -abayes -lbp 1000
Seed:    158418 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Thu Apr 24 17:23:57 2025
Kernel:  SSE2 - 1 threads (12 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 12 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading alignment file /var/folders/1t/w4ys4pks4q5d5_kl7svl4t080000gn/T/qiime2/jgc/data/d34420d9-336e-4d9e-aee8-99e64b3315f0/data/aligned-dna-sequences.fasta ... Fasta format detected
Reading fasta file: done in 9.10759e-05 secs using 84.54% CPU
Alignment most likely contains DNA/RNA sequences
Alignment has 20 sequences with 214 columns, 157 distinct patterns
104 parsimony-informative, 33 singleton sites, 77 constant sites
                                          Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 7.86781e-06 secs using 76.26% CPU
   1  e84fcf85a6a4065231dcf343bb862f1cb32abae6   40.65%    passed     90.91%
   2  5525fb6dab7b6577960147574465990c6df070ad   42.99%    passed     99.80%
   3  eb3564a35320b53cef22a77288838c7446357327   42.99%    passed     25.49%
   4  418f1d469f08c99976b313028cf6d3f18f61dd55   43.93%    passed     71.86%
   5  2e3b2c075901640c4de739473f9246385430b1ed   31.31%    passed     90.76%
   6  0469f8d819bd45c7638d1c8b0895270a05f34267   38.79%    passed     92.82%
   7  d162ed685007f5adede58f14aece31dfa1b60c18   40.65%    passed     97.17%
   8  1d45b2bce36cd995c5dcb755babf512e612ce8b9   41.59%    passed     39.04%
   9  5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8   31.31%    passed     87.21%
  10  206656bec2abdbc4aee37a661ef5f4a62b5dd6ae   42.99%    passed     85.00%
  11  606c23e79bb730ad74e3c6efd72004c36674c17a   47.20%    passed     87.78%
  12  682e91d7e510ab134d0625234ad224f647c14eb0   41.59%    passed     31.01%
  13  6a36152105590b1eb095b9503e8f1f226fc73e43   39.25%    passed     86.29%
  14  6ca685c39a33bfbcb3123129e7af88d573df7d6f   42.06%    failed      0.02%
  15  8a1c44eb462ed58b21f3fdd72dd22bb657db2980   31.78%    passed     54.40%
  16  9b220cae8d375ea38b8b481cb95949cda8722fcb   36.92%    passed     88.78%
  17  aa4698d2e2b1fa71d08e2934a923aad7374a18f6   37.85%    passed     90.52%
  18  b31aa3f04bc9d5e2498d45cf1983dfaf09faa258   31.78%    passed     72.69%
  19  d44b129a6181f052198bda3813f0802a91612441   41.59%    passed     41.69%
  20  ed1acad8a98e8579a44370733533ad7d3fed8006   48.13%    passed     58.15%
****  TOTAL                                      39.77%  1 sequences failed composition chi2 test (p-value<5%; df=3)

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.000 seconds
```

--------------------------------

### IQ-TREE Ultrafast Bootstrap Command Line Usage

Source: https://docs.qiime2.org/2024.10/plugins/available/phylogeny/iqtree-ultrafast-bootstrap

Displays the command line interface options for the iqtree-ultrafast-bootstrap plugin.

```bash
Usage: qiime phylogeny iqtree-ultrafast-bootstrap [OPTIONS]

  Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
  automatic model selection and bootstrap supports.

Inputs:
  --i-alignment ARTIFACT FeatureData[AlignedSequence]
                          Aligned sequences to be used for phylogenetic
                          reconstruction.                           [required]
Parameters:
  --p-seed INTEGER        Random number seed. If not set, program defaults
                          will be used. See IQ-TREE manual for details.
                                                                    [optional]
  --p-n-cores NTHREADS    The number of cores to use for parallel processing.
                          Use `auto` to let IQ-TREE automatically determine
                          the optimal number of cores to use.     [default: 1]
  --p-n-cores-max NTHREADS
                          Limits the maximum number of cores to be used when
                          'n-cores' is set to 'auto'.               [optional]
  --p-n-runs INTEGER      Number of indepedent runs. Multiple  independent
    Range(1, None)        runs (e.g. 10) can outperform a single run in terms
                          of likelihood maximisation.             [default: 1]
  --p-substitution-model TEXT Choices('JC', 'JC+I', 'JC+G', 'JC+I+G',
    'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9',
    'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3',
    'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10',
    'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4',
    'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY',
    'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5',
    'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I',
    'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6',
    'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G',
    'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9',
    'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3',
    'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10',
    'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4',
    'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2',
    'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4',
    'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10',
    'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3',
    'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9',
    'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3',
```

--------------------------------

### CLI Usage for Heatmap

Source: https://docs.qiime2.org/2024.10/plugins/available/vizard/heatmap

Example command to generate a heatmap visualization from a metadata file.

```bash
qiime vizard heatmap \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-gradient-measure a \
  --o-visualization heatmap.qzv
```

--------------------------------

### Update Conda

Source: https://docs.qiime2.org/2024.10/install/native

Ensures the conda package manager is running the latest version after installation.

```bash
conda update conda
```

--------------------------------

### Run Alpha Group Significance

Source: https://docs.qiime2.org/2024.10/plugins/available/stats/alpha-group-significance

Examples of executing the alpha-group-significance command with and without repeated measures.

```bash
qiime stats alpha-group-significance \
  --i-alpha-diversity alpha-div-faith-pd.qza \
  --m-metadata-file metadata.tsv \
  --p-columns genotype donor_status \
  --p-subject mouse_id \
  --p-timepoint days_post_transplant \
  --o-distribution dist.qza \
  --o-stats stats.qza \
  --o-raincloud raincloud.qzv
qiime stats alpha-group-significance \
  --i-alpha-diversity alpha-div-faith-pd.qza \
  --m-metadata-file metadata.tsv \
  --p-columns genotype donor_status \
  --o-distribution dist2.qza \
  --o-stats stats2.qza \
  --o-raincloud raincloud2.qzv
```

--------------------------------

### Download metadata via command line

Source: https://docs.qiime2.org/2024.10/tutorials/moving-pictures-usage

Uses wget to download the sample metadata file directly to the local filesystem.

```bash
wget \
  -O 'sample-metadata.tsv' \
  'https://docs.qiime2.org/2024.10/data/tutorials/moving-pictures-usage/sample-metadata.tsv'
```

--------------------------------

### Access command help

Source: https://docs.qiime2.org/2024.10/interfaces/q2cli

Use the --help flag to view documentation for specific plugins or commands.

```bash
qiime feature-table --help
```

--------------------------------

### Alpha Rarefaction Analysis

Source: https://docs.qiime2.org/2024.10/tutorials/moving-pictures-usage

Examples of invoking the alpha-rarefaction visualizer across different QIIME 2 interfaces.

```python
alpha_rarefaction_viz, = diversity_actions.alpha_rarefaction(
    table=table,
    phylogeny=rooted_tree,
    max_depth=4000,
    metadata=sample_metadata_md,
)
```

```r
action_results <- diversity_actions$alpha_rarefaction(
    table=table,
    phylogeny=rooted_tree,
    max_depth=4000L,
    metadata=sample_metadata_md,
)
alpha_rarefaction_viz <- action_results$visualization
```

```bash
qiime diversity alpha-rarefaction \
  --i-table table.qza \
  --i-phylogeny phylogeny-align-to-tree-mafft-fasttree/rooted_tree.qza \
  --p-max-depth 4000 \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization alpha-rarefaction.qzv
```

```python
use.action(
    use.UsageAction(plugin_id='diversity', action_id='alpha_rarefaction'),
    use.UsageInputs(table=table_dada2, phylogeny=rooted_tree,
                    max_depth=4000, metadata=sample_metadata),
    use.UsageOutputNames(visualization='alpha_rarefaction'),
)
```

--------------------------------

### Command line usage for plot-rainclouds

Source: https://docs.qiime2.org/2024.10/plugins/available/stats/plot-rainclouds

Example command to generate a raincloud plot visualization from a distribution artifact.

```bash
qiime stats plot-rainclouds \
  --i-data dist.qza \
  --o-visualization raincloud-plot.qzv
```

--------------------------------

### Inspect manifest file

Source: https://docs.qiime2.org/2024.10/tutorials/pd-mice

Check the first few lines of the sample manifest file to verify its structure.

```bash
head manifest.tsv
```

--------------------------------

### Compute Weighted UniFrac

Source: https://docs.qiime2.org/2024.10/plugins/available/diversity-lib/weighted-unifrac

Examples of running the weighted-unifrac command with various thread configurations and optimization settings.

```bash
qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --o-distance-matrix weighted-unifrac-dm.qza
```

```bash
qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads 1 \
  --o-distance-matrix weighted-unifrac-dm.qza
```

```bash
qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --o-distance-matrix weighted-unifrac-dm.qza
```

```bash
qiime diversity-lib weighted-unifrac \
  --i-table feature-table.qza \
  --i-phylogeny phylogeny.qza \
  --p-threads auto \
  --p-bypass-tips \
  --o-distance-matrix weighted-unifrac-dm.qza
```

--------------------------------

### Download manifest file

Source: https://docs.qiime2.org/2024.10/tutorials/pd-mice

Download the sample manifest file using either wget or curl.

```bash
wget \
  -O "manifest.tsv" \
  "https://data.qiime2.org/2024.10/tutorials/pd-mice/manifest"
```

```bash
curl -sL \
  "https://data.qiime2.org/2024.10/tutorials/pd-mice/manifest" > \
  "manifest.tsv"
```

--------------------------------

### Activate QIIME 2 Environment

Source: https://docs.qiime2.org/2024.10/install/native

Activates the installed QIIME 2 environment using its specific name.

```bash
conda activate qiime2-<distro>-2024.10
```

--------------------------------

### Command line interface for partition-samples-single

Source: https://docs.qiime2.org/2024.10/plugins/available/demux/partition-samples-single

Displays the usage, inputs, parameters, and outputs for the command line interface.

```bash
Usage: qiime demux partition-samples-single [OPTIONS]

  Partition demultiplexed single end sequences into individual samples or the
  number of partitions specified.

Inputs:
  --i-demux ARTIFACT SampleData[SequencesWithQuality¹ |
    JoinedSequencesWithQuality²]
                         The demultiplexed sequences to partition.  [required]
Parameters:
  --p-num-partitions INTEGER
    Range(1, None)       The number of partitions to split the demultiplexed
                         sequences into. Defaults to partitioning into
                         individual samples.                        [optional]
Outputs:
  --o-partitioned-demux ARTIFACTS...
    Collection[SampleData[SequencesWithQuality¹ |
    JoinedSequencesWithQuality²]]
                         The partitioned demultiplexed sequences.   [required]
Miscellaneous:
  --output-dir PATH      Output unspecified results to a directory
  --verbose / --quiet    Display verbose output to stdout and/or stderr
                         during execution of this action. Or silence output if
                         execution is successful (silence is golden).
  --example-data PATH    Write example data and exit.
  --citations            Show citations and exit.
  --use-cache DIRECTORY  Specify the cache to be used for the intermediate
                         work of this action. If not provided, the default
                         cache under $TMP/qiime2/ will be used.
                         IMPORTANT FOR HPC USERS: If you are on an HPC system
                         and are using parallel execution it is important to
                         set this to a location that is globally accessible to
                         all nodes in the cluster.
  --help                 Show this message and exit.
```

--------------------------------

### RAxML Rapid Bootstrap CLI Usage

Source: https://docs.qiime2.org/2024.10/plugins/available/phylogeny/raxml-rapid-bootstrap

Displays the command-line interface options and parameters for running the raxml-rapid-bootstrap method.

```bash
Usage: qiime phylogeny raxml-rapid-bootstrap [OPTIONS]

  Construct a phylogenetic tree with RAxML with the addition of rapid
  bootstrapping support values. See:
  https://sco.h-its.org/exelixis/web/software/raxml/

Inputs:
  --i-alignment ARTIFACT FeatureData[AlignedSequence]
                          Aligned sequences to be used for phylogenetic
                          reconstruction.                           [required]
Parameters:
  --p-seed INTEGER        Random number seed for the parsimony starting tree.
                          This allows you to reproduce tree results. If not
                          supplied then one will be randomly chosen.
                                                                    [optional]
  --p-rapid-bootstrap-seed INTEGER
                          Specify a random seed for rapid bootstrapping. This
                          allows you to reproduce rapid bootstrap results. If
                          not supplied then one will be randomly chosen.
                                                                    [optional]
  --p-bootstrap-replicates INTEGER
    Range(10, None)       The number of bootstrap searches to perform.
                                                                [default: 100]
  --p-n-threads NTHREADS  The number of threads to use for multithreaded
                          processing. Using more than one thread will enable
                          the PTHREADS version of RAxML.          [default: 1]
  --p-raxml-version TEXT Choices('Standard', 'SSE3', 'AVX2')
                          Select a specific CPU optimization of RAxML to use.
                          The SSE3 versions will run approximately 40% faster
                          than the standard version. The AVX2 version will run
                          10-30% faster than the SSE3 version.
                                                         [default: 'Standard']
  --p-substitution-model TEXT Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT',
    'GTRCATI')            Model of Nucleotide Substitution
                                                         [default: 'GTRGAMMA']
Outputs:
  --o-tree ARTIFACT       The resulting phylogenetic tree.
    Phylogeny[Unrooted]                                             [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --use-cache DIRECTORY   Specify the cache to be used for the intermediate
                          work of this action. If not provided, the default
                          cache under $TMP/qiime2/ will be used.
                          IMPORTANT FOR HPC USERS: If you are on an HPC system
                          and are using parallel execution it is important to
                          set this to a location that is globally accessible
                          to all nodes in the cluster.
  --help                  Show this message and exit.
```

--------------------------------

### Run scatterplot-2d via CLI

Source: https://docs.qiime2.org/2024.10/plugins/available/vizard/scatterplot-2d

Examples of using the scatterplot-2d command with default settings and with specific measures and color grouping.

```bash
qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --o-visualization scatterplot.qzv
```

```bash
qiime vizard scatterplot-2d \
  --m-metadata-file metadata.tsv \
  --p-x-measure x \
  --p-y-measure y \
  --p-color-by group \
  --o-visualization scatterplot.qzv
```

--------------------------------

### Download qc-mock-3-expected.qza

Source: https://docs.qiime2.org/2024.10/tutorials/quality-control

Download the expected mock community composition artifact using wget or curl.

```bash
wget \
  -O "qc-mock-3-expected.qza" \
  "https://data.qiime2.org/2024.10/tutorials/quality-control/qc-mock-3-expected.qza"
```

```bash
curl -sL \
  "https://data.qiime2.org/2024.10/tutorials/quality-control/qc-mock-3-expected.qza" > \
  "qc-mock-3-expected.qza"
```

--------------------------------

### Execute IQ-TREE with default settings

Source: https://docs.qiime2.org/2024.10/tutorials/phylogeny

Run the IQ-TREE method using default parameters and automatic model selection (MFP).

```bash
qiime phylogeny iqtree \
  --i-alignment masked-aligned-rep-seqs.qza \
  --o-tree iqt-tree.qza \
  --verbose
```
Tokens:
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