### Install Homebrew and Nonpareil

Source: https://nonpareil.readthedocs.io/en/latest/installation.html

Commands to set up Homebrew, add the bio tap, and install the software.

```bash
$ /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
```

```bash
$ brew tap brewsci/bio
```

```bash
$ brew install nonpareil
```

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

### Run Package Examples

Source: https://nonpareil.readthedocs.io/en/latest/curves.html

Commands to execute built-in package examples using provided sample data.

```R
example(Nonpareil.curve);
example(Nonpareil.set);
```

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

### Install compiled binaries

Source: https://nonpareil.readthedocs.io/en/latest/installation.html

Commands to install the compiled software system-wide or to a custom directory.

```bash
sudo make install
```

```bash
make prefix=$HOME/apps install
```

```bash
make prefix=$HOME R=~/bin/R install
```

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

### Prepare Sample Data Table

Source: https://nonpareil.readthedocs.io/en/latest/curves.html

Example of a tab-delimited text file structure for organizing multiple .npo files.

```text
# samples.txt
File        Name    Col
SRS063417.1.L50.npo Posterior fornix        "#FFC8C8"
SRS063287.1.L50.npo Buccal mucosa   "#FF7878"
SRS062540.1.L50.npo Tongue dorsum   "#FF0303"
SRS016335.1.L50.npo Stool   "#C8874C"
SRS015574.1.L50.npo Supragingival plaque    "#E66478"
SRS019087.1.L50.npo Anterior nares  "#DCDC82"
```

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

### Install and Load Nonpareil

Source: https://nonpareil.readthedocs.io/en/latest/curves.html

Commands to install the package from CRAN and load it into the R environment.

```R
install.packages('Nonpareil');
library(Nonpareil);
```

```R
library(Nonpareil);
```

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

### Run Nonpareil analysis

Source: https://nonpareil.readthedocs.io/en/latest/redundancy.html

Basic command-line examples for executing Nonpareil with different algorithms, file formats, and compression settings.

```bash
# fastq is recommended for kmer algorithm
nonpareil -s reads.fa -T kmer -f fastq -b output
nonpareil -s reads.fa -T kmer -f fasta -b output

# fasta is recommended for alignment algorithm
nonpareil -s reads.fa -T alignment -f fasta -b output
nonpareil -s reads.fa -T alignment -f fastq -b output

# gzipped files are also supported (with .gz extension)
nonpareil -s reads.fa.gz -T kmer -f fastq -b output
```

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

### Configure Conda channels

Source: https://nonpareil.readthedocs.io/en/latest/installation.html

Set up the required channels for Bioconda installation.

```bash
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
```

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

### Install Nonpareil via Conda

Source: https://nonpareil.readthedocs.io/en/latest/installation.html

Install the Nonpareil package using the conda package manager.

```bash
conda install nonpareil
```

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

### Compile Nonpareil with MPI

Source: https://nonpareil.readthedocs.io/en/latest/mpi.html

Build the MPI-enabled binary from the source directory.

```bash
cd nonpareil # or wherever you have the nonpareil folder
make nonpareil-mpi
```

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

### Convert FastQ to FastA

Source: https://nonpareil.readthedocs.io/en/latest/preprocess.html

Use this command to transform FastQ files into FastA format for compatibility with Nonpareil.

```bash
# Input: reads.fastq
# Output: reads.fasta
cat reads.fastq | paste - - - - | awk 'BEGIN{FS="\t"}{print ">"substr($1,2)"\n"$2}' > reads.fasta
```

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

### Generate host file for MPI

Source: https://nonpareil.readthedocs.io/en/latest/mpi.html

Create a list of machine names for the MPI cluster using the PBS node file.

```bash
cat $PBS_NODEFILE | awk 'NR%16==0' > hosts.txt # Change the '16' by the number of CPUs you are using (the value of ppn).
```

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

### View Function Documentation

Source: https://nonpareil.readthedocs.io/en/latest/curves.html

Commands to open the help pages for curve and set plotting functions.

```R
?Nonpareil.curve
```

```R
?Nonpareil.set
```

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

### Compile Nonpareil from source

Source: https://nonpareil.readthedocs.io/en/latest/installation.html

Standard compilation commands for Nonpareil and the MPI-enabled version.

```bash
cd nonpareil
make
```

```bash
make nonpareil-mpi
```

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

### Access Nonpareil Help

Source: https://nonpareil.readthedocs.io/en/latest/curves.html

Commands to view documentation for specific Nonpareil functions within R.

```R
?Nonpareil.curve
?Nonpareil.set
?Nonpareil.legend
?Nonpareil.predict
```

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

### Download source code

Source: https://nonpareil.readthedocs.io/en/latest/installation.html

Methods to obtain the Nonpareil source code via git or tarball.

```bash
git clone git://github.com/lmrodriguezr/nonpareil.git
```

```bash
tar zxvf nonpareil.tar.gz
```

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

### Execute Nonpareil with MPI

Source: https://nonpareil.readthedocs.io/en/latest/mpi.html

Run the MPI binary using mpirun, specifying the machine file and thread count per machine.

```bash
mpirun -np 10 -machinefile hosts.txt nonpareil-mpi -t 16 -s path/to/your/sequences.fasta -b output ...
```

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

### Pull and run Nonpareil Docker container

Source: https://nonpareil.readthedocs.io/en/latest/installation.html

Commands to download and execute the Nonpareil Biocontainer.

```bash
$ docker pull quay.io/biocontainers/nonpareil
```

```bash
$ docker run -i -t quay.io/biocontainers/nonpareil /bin/bash
```

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

### Compile with custom compiler

Source: https://nonpareil.readthedocs.io/en/latest/installation.html

Specify the C++ compiler path during the compilation process.

```bash
# This compiles nonpareil with /usr/local/bin/g++
make cpp=/usr/local/bin/g++ nonpareil
# This compiles nonpareil-mpi with /usr/local/bin/mpic++
make mpicpp=/usr/local/bin/mpic++ nonpareil-mpi
```

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

### nonpareil

Source: https://nonpareil.readthedocs.io/en/latest/redundancy.html

The main command-line interface for running Nonpareil redundancy analysis.

```APIDOC
## nonpareil

### Description
Executes the Nonpareil redundancy analysis on a sequence file using either k-mer or alignment algorithms.

### Parameters
#### Mandatory Options
- **-s** (str) - Required - Path to the input file containing sequences (supports .gz).
- **-T** (str) - Required - Nonpareil algorithm to use: 'kmer' or 'alignment'.
- **-f** (str) - Required - Format of the sequence: 'fasta' or 'fastq'.

#### Common Options
- **-b** (str) - Optional - Path prefix for all output files.
- **-d** (num) - Optional - Subsample factor for logarithmic subsampling (default: 0.7).
- **-n** (int) - Optional - Number of sub-samples to generate per point (default: 1024).
- **-L** (num) - Optional - Minimum overlapping percentage of the aligned region (default: 50).
- **-X** (int) - Optional - Maximum number of reads to use as query (default: 1000).
- **-q** (str) - Optional - Path to a second dataset for comparison (experimental).
- **-R** (int) - Optional - Maximum RAM usage in MiB (default: 1024).
- **-t** (int) - Optional - Number of threads (default: 2).
- **-v** (int) - Optional - Verbosity level (default: 7).
- **-V** (flag) - Optional - Show version information and exit.
- **-h** (flag) - Optional - Display help message and exit.
```

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

### Plot Multiple Curves with Nonpareil.set

Source: https://nonpareil.readthedocs.io/en/latest/curves.html

Workflow to read a sample table and generate a combined plot for multiple datasets.

```R
library(Nonpareil);
samples <- read.table('samples.txt', sep='\t', header=TRUE, as.is=TRUE);
attach(samples);
nps <- Nonpareil.set(File, col=Col, labels=Name, plot.opts=list(plot.observed=FALSE));
detach(samples);
summary(nps);
```

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

### Generate a Single Nonpareil Curve

Source: https://nonpareil.readthedocs.io/en/latest/curves.html

Basic command to plot a curve from a single .npo redundancy file.

```R
Nonpareil.curve('output.npo'); # Change output.npo to the actual redundancy file.
```

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

### Split paired-end reads

Source: https://nonpareil.readthedocs.io/en/latest/preprocess.html

Use this script to separate interposed paired-end reads into individual files.

```perl
# Input: reads.fasta
# Output: reads.1.fa and reads.2.fa
FastA.split.pl reads.fasta reads 2
```

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