### Build Trimmomatic from Source

Source: https://github.com/usadellab/trimmomatic/blob/main/README.md

Use this command to build Trimmomatic from its source code using Apache Maven. Ensure you have JDK 8 or higher installed.

```bash
mvn clean package
```

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

### Paired-End Trimming (Less Sensitive Adapters)

Source: https://github.com/usadellab/trimmomatic/blob/main/README.md

This command is a reference for paired-end trimming with adapter clipping, using ILLUMINACLIP, LEADING, TRAILING, SLIDINGWINDOW, and MINLEN. It is less sensitive for adapter detection compared to the previous example.

```java
java -jar trimmomatic-0.39.jar PE \
input_forward.fq.gz input_reverse.fq.gz \
output_forward_paired.fq.gz output_forward_unpaired.fq.gz \
output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz \
ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
```

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

### Leading and Trailing Quality Trimming

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Removes low-quality bases from the start (LEADING) or end (TRAILING) of reads based on a quality threshold. Use specific quality values for desired stringency.

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  LEADING:3 \
  TRAILING:3
```

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  LEADING:20 \
  TRAILING:20 \
  MINLEN:50
```

```bash
java -jar trimmomatic-0.40.jar PE \
  input_R1.fq.gz input_R2.fq.gz \
  out_1P.fq.gz out_1U.fq.gz out_2P.fq.gz out_2U.fq.gz \
  ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 \
  LEADING:3 \
  TRAILING:3 \
  SLIDINGWINDOW:4:15 \
  MINLEN:36
```

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

### Crop Fixed Length Retention

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Trims reads to a specified maximum length, retaining bases from the start. Useful for standardizing read lengths for specific analyses.

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  CROP:100
```

```bash
java -jar trimmomatic-0.40.jar PE \
  input_R1.fq.gz input_R2.fq.gz \
  out_1P.fq.gz out_1U.fq.gz out_2P.fq.gz out_2U.fq.gz \
  CROP:75 \
  MINLEN:50
```

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

### Headcrop and Tailcrop Fixed Length Trimming

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Removes a fixed number of bases from the start (HEADCROP) or end (TAILCROP) of reads. Useful for removing technical sequences or low-quality regions.

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  HEADCROP:10
```

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  TAILCROP:5
```

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  HEADCROP:12 \
  TAILCROP:8 \
  MINLEN:50
```

```bash
java -jar trimmomatic-0.40.jar PE \
  input_R1.fq.gz input_R2.fq.gz \
  out_1P.fq.gz out_1U.fq.gz out_2P.fq.gz out_2U.fq.gz \
  HEADCROP:15 \
  ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 \
  MINLEN:36
```

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

### Build Trimmomatic from Source

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Instructions for cloning the repository and building the project using Maven.

```bash
# Clone repository and build
git clone https://github.com/usadellab/Trimmomatic.git
cd Trimmomatic

# Build with Maven (requires JDK 8+)
mvn clean package

# The JAR file will be in target/trimmomatic-0.40.jar
# The distribution ZIP will be in target/Trimmomatic-0.40.zip

# Run tests
mvn test

# Run the built JAR
java -jar target/trimmomatic-0.40.jar -version
```

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

### Single End Mode Command Line

Source: https://github.com/usadellab/trimmomatic/blob/main/README.md

Use this command for processing single-ended FASTQ files. Specify input and output files along with desired trimming steps.

```bash
java -jar <path to trimmomatic jar> SE [-threads <threads>] [-phred33 | -phred64] \
[-trimlog <logFile>] [-summary <summaryFile>] [-compressLevel <level>] [-compressStream | -compressBlock] [-quiet] [-version] \
<input> <output> \
<step 1> # Additional steps added as needed
```

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

### Manage Trimmomatic with Docker

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Commands for building the Trimmomatic Docker image and executing trimming tasks within containers.

```bash
# Build Docker image
docker build --build-arg TRIMMOMATIC_VERSION=0.40 -t trimmomatic:0.40 .

# Run version check
docker run trimmomatic:0.40

# Run paired-end trimming with mounted volumes
docker run -v /path/to/data:/data trimmomatic:0.40 PE \
  -threads 4 \
  /data/input_R1.fq.gz /data/input_R2.fq.gz \
  /data/out_1P.fq.gz /data/out_1U.fq.gz \
  /data/out_2P.fq.gz /data/out_2U.fq.gz \
  ILLUMINACLIP:/opt/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 \
  SLIDINGWINDOW:4:15 MINLEN:36

# Run single-end trimming
docker run -v /path/to/data:/data trimmomatic:0.40 SE \
  -threads 4 \
  /data/input.fq.gz /data/output.fq.gz \
  ILLUMINACLIP:/opt/trimmomatic/adapters/TruSeq3-SE.fa:2:30:10 \
  MINLEN:36
```

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

### Paired End Mode Command Line

Source: https://github.com/usadellab/trimmomatic/blob/main/README.md

Use this command for processing paired-end FASTQ files. Specify input and output files along with desired trimming steps.

```bash
java -jar <path to trimmomatic.jar> PE [-threads <threads] [-phred33 | -phred64] \
[-trimlog <logFile>] [-summary <summaryFile>] [-basein <templateInputFile>] [-baseout <templateOutputFile>] \
[-validatePairs] [-compressLevel <level>] [-compressStream | -compressBlock] [-quiet] [-version] \
<input 1> <input 2> \
<paired output 1> <unpaired output 1> \
<paired output 2> <unpaired output 2> \
<step 1> # Additional steps added as needed
```

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

### Paired-End Adapter Clipping (Standard)

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Standard paired-end adapter clipping using a specified FASTA file and parameters for seed mismatches, palindrome threshold, simple threshold, and minimum adapter length. 'keepBothReads' is set to True.

```bash
java -jar trimmomatic-0.40.jar PE \
  input_R1.fq.gz input_R2.fq.gz \
  out_1P.fq.gz out_1U.fq.gz out_2P.fq.gz out_2U.fq.gz \
  ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True
```

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

### Paired-End Trimming with Adapter Clipping

Source: https://github.com/usadellab/trimmomatic/blob/main/README.md

This command performs paired-end trimming with adapter clipping using the ILLUMINACLIP, LEADING, TRAILING, and MINLEN options. The `keepBothReads` parameter is set to True, and the minimum adapter length is specified.

```java
java -jar trimmomatic-0.39.jar PE \
input_forward.fq.gz input_reverse.fq.gz \
output_forward_paired.fq.gz output_forward_unpaired.fq.gz \
output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz \
ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36
```

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

### Paired-End Adapter Clipping (Nextera)

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Adapter clipping for paired-end reads using Nextera library preparation adapters. Includes parameters for seed mismatches, palindrome threshold, simple threshold, minimum adapter length, and 'keepBothReads'.

```bash
java -jar trimmomatic-0.40.jar PE \
  input_R1.fq.gz input_R2.fq.gz \
  out_1P.fq.gz out_1U.fq.gz out_2P.fq.gz out_2U.fq.gz \
  ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:True
```

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

### Single-End Trimming with Adapter Clipping

Source: https://github.com/usadellab/trimmomatic/blob/main/README.md

This command performs single-ended trimming with adapter clipping using ILLUMINACLIP, LEADING, TRAILING, SLIDINGWINDOW, and MINLEN. It is suitable for single-ended sequencing data.

```java
java -jar trimmomatic-0.39.jar SE \
input.fq.gz \
output.fq.gz \
ILLUMINACLIP:TruSeq3-SE:2:30:10 \
LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
```

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

### Basic Paired-End Trimming

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Performs paired-end trimming with adapter removal and quality filtering. Requires specifying input and output files, adapter sequences, and quality thresholds.

```bash
java -jar trimmomatic-0.40.jar PE \
  -threads 4 \
  -phred33 \
  -trimlog trim.log \
  -summary stats.txt \
  input_R1.fastq.gz input_R2.fastq.gz \
  output_R1_paired.fastq.gz output_R1_unpaired.fastq.gz \
  output_R2_paired.fastq.gz output_R2_unpaired.fastq.gz \
  ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True \
  LEADING:3 \
  TRAILING:3 \
  SLIDINGWINDOW:4:15 \
  MINLEN:36
```

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

### Execute NGS Processing Pipelines

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Common workflows for RNA-seq, Whole Genome Sequencing, and Amplicon sequencing trimming.

```bash
# RNA-seq paired-end preprocessing pipeline
java -jar trimmomatic-0.40.jar PE \
  -threads 8 \
  -phred33 \
  -trimlog rna_trim.log \
  -summary rna_stats.txt \
  sample_R1.fastq.gz sample_R2.fastq.gz \
  sample_R1_paired.fq.gz sample_R1_unpaired.fq.gz \
  sample_R2_paired.fq.gz sample_R2_unpaired.fq.gz \
  ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:2:True \
  LEADING:3 \
  TRAILING:3 \
  SLIDINGWINDOW:4:15 \
  MINLEN:36

# Whole genome sequencing pipeline with aggressive filtering
java -jar trimmomatic-0.40.jar PE \
  -threads 16 \
  -validatePairs \
  wgs_R1.fq.gz wgs_R2.fq.gz \
  wgs_R1_P.fq.gz wgs_R1_U.fq.gz wgs_R2_P.fq.gz wgs_R2_U.fq.gz \
  ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True \
  LEADING:20 \
  TRAILING:20 \
  SLIDINGWINDOW:5:20 \
  AVGQUAL:25 \
  MINLEN:50

# Amplicon sequencing with fixed-length output
java -jar trimmomatic-0.40.jar PE \
  -threads 4 \
  amplicon_R1.fq.gz amplicon_R2.fq.gz \
  amp_R1_P.fq.gz amp_R1_U.fq.gz amp_R2_P.fq.gz amp_R2_U.fq.gz \
  ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 \
  HEADCROP:20 \
  CROP:250 \
  MINLEN:100
```

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

### Paired-End Trimming Pipeline

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Combines adapter trimming, sliding window, and minimum length filtering for paired-end reads. Ensure input and output files are correctly specified.

```bash
java -jar trimmomatic-0.40.jar PE \
  input_R1.fq.gz input_R2.fq.gz \
  out_1P.fq.gz out_1U.fq.gz out_2P.fq.gz out_2U.fq.gz \
  ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 \
  SLIDINGWINDOW:4:15 \
  MINLEN:36
```

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

### Paired-End Trimming with Template Naming

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Uses a base input and base output name for paired-end trimming, simplifying file naming conventions. Adapter clipping and minimum length filtering are applied.

```bash
java -jar trimmomatic-0.40.jar PE \
  -threads 4 \
  -basein sample_R1.fastq.gz \
  -baseout sample_trimmed.fastq.gz \
  ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True \
  MINLEN:36
```

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

### Paired-End Adapter Clipping (TruSeq2)

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Adapter clipping for paired-end reads using TruSeq2 adapters, suitable for older GAII machines. Specifies adapter FASTA file, seed mismatches, and palindrome/simple thresholds.

```bash
java -jar trimmomatic-0.40.jar PE \
  input_R1.fq.gz input_R2.fq.gz \
  out_1P.fq.gz out_1U.fq.gz out_2P.fq.gz out_2U.fq.gz \
  ILLUMINACLIP:TruSeq2-PE.fa:2:30:10
```

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

### Basic Single-End Trimming

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Performs basic single-end trimming with adapter removal and quality filtering. Specify input and output files, adapter sequences, and quality thresholds.

```bash
java -jar trimmomatic-0.40.jar SE \
  -threads 4 \
  -phred33 \
  -trimlog trim.log \
  -summary stats.txt \
  input.fastq.gz \
  output.fastq.gz \
  ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 \
  LEADING:3 \
  TRAILING:3 \
  SLIDINGWINDOW:4:15 \
  MINLEN:36
```

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

### Single-End Adapter Clipping

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Performs adapter clipping on single-end reads using a specified FASTA file and parameters for seed mismatches, palindrome threshold, and simple threshold.

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  ILLUMINACLIP:TruSeq3-SE.fa:2:30:10
```

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

### Sliding Window Quality Trimming (Standard)

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Applies sliding window quality trimming to single-end reads. Uses a 4-base window and a quality threshold of 15 to determine where to trim.

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  SLIDINGWINDOW:4:15
```

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

### Maxinfo Adaptive Quality Trimming

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Trims reads using an adaptive algorithm that balances read length and error rate to maximize read value. Adjust strictness for quality vs. length focus.

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  MAXINFO:50:0.5
```

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  MAXINFO:75:0.8
```

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  MAXINFO:100:0.2
```

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

### Trimmomatic Processing Steps

Source: https://github.com/usadellab/trimmomatic/blob/main/README.md

Detailed configuration options for various read trimming and filtering operations.

```APIDOC
## ILLUMINACLIP

### Description
Performs adapter clipping on sequencing reads.

### Parameters
- **fastaWithAdaptersEtc** (string) - Required - Path to fasta file containing adapters.
- **seedMismatches** (int) - Required - Maximum mismatch count for full match.
- **palindromeClipThreshold** (int) - Required - Accuracy threshold for PE palindrome alignment.
- **simpleClipThreshold** (int) - Required - Accuracy threshold for simple adapter matching.
- **minAdapterLengthPalindrome** (int) - Optional - Minimum adapter length in palindrome mode [default = 8].
- **keepBothReads** (boolean) - Optional - Keep both reads in palindrome mode [default = False].

## LEADING / TRAILING

### Description
Removes bases from the start (LEADING) or end (TRAILING) of the read if they fall below the specified quality.

### Parameters
- **quality** (int) - Required - Minimum quality required to keep a base.

## HEADCROP / TAILCROP / CROP

### Description
Removes a fixed number of bases from the start (HEADCROP) or end (TAILCROP) of the read, or keeps a fixed length from the start (CROP).

### Parameters
- **length** (int) - Required - Number of bases to remove or keep.

## SLIDINGWINDOW

### Description
Performs a sliding window trim, cutting once the average quality within the window falls below a threshold.

### Parameters
- **windowSize** (int) - Required - Number of bases to average across.
- **requiredQuality** (int) - Required - Average quality required.

## MAXINFO

### Description
Trims reads based on a scoring system favoring a target length while maintaining quality.

### Parameters
- **targetLength** (int) - Required - Ideal length for a read.
- **strictness** (float) - Required - Trade-off between length and quality (0.0 to 1.0).

## MINLEN / MAXLEN / AVGQUAL

### Description
Filters reads based on length (MINLEN/MAXLEN) or average Phred quality score (AVGQUAL).

### Parameters
- **length/quality** (int) - Required - Threshold value.

## BASECOUNT

### Description
Filters reads based on the frequency of specific characters.

### Parameters
- **bases** (string) - Required - Characters to count (e.g., N, GC).
- **minCount** (int) - Optional - Minimum occurrences.
- **maxCount** (int) - Optional - Maximum occurrences.

## TOPHRED33 / TOPHRED64

### Description
Forces the input quality encoding to Phred 33 or Phred 64.
```

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

### Single End Mode with Explicit Class

Source: https://github.com/usadellab/trimmomatic/blob/main/README.md

Alternative command for single-end processing using the explicit Java class. Functionality is identical to the -jar method.

```bash
java -classpath <path to trimmomatic jar> org.usadellab.trimmomatic.TrimmomaticSE [-threads <threads>] [-phred33 | -phred64] \
[-trimlog <logFile>] [-summary <summaryFile>] [-compressLevel <level>] [-compressStream | -compressBlock] [-quiet] [-version] \
<input> <output> \
<step 1> # Additional steps added as needed
```

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

### Paired End Mode with Explicit Class

Source: https://github.com/usadellab/trimmomatic/blob/main/README.md

Alternative command for paired-end processing using the explicit Java class. Functionality is identical to the -jar method.

```bash
java -classpath <path to trimmomatic jar> org.usadellab.trimmomatic.TrimmomaticPE [-threads <threads>] [-phred33 | -phred64] \
[-trimlog <logFile>] [-summary <summaryFile>] [-basein <templateInputFile>] [-baseout <templateOutputFile>] \
[-validatePairs] [-compressLevel <level>] [-compressStream | -compressBlock] [-quiet] [-version] \
<input 1> <input 2> \
<paired output 1> <unpaired output 1> \
<paired output 2> <unpaired output 2> \
<step 1> # Additional steps added as needed
```

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

### Convert Phred-33 to Phred-64

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Use this command to convert sequencing data quality scores between Phred-33 and Phred-64 formats.

```bash
java -jar trimmomatic-0.40.jar SE \
  -phred33 \
  input_phred33.fq.gz output_phred64.fq.gz \
  TOPHRED64
```

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

### Minimal Single-End Trimming for Quality

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Applies minimal trimming to single-end reads, focusing solely on quality filtering based on average quality score and minimum read length. No adapter trimming is performed.

```bash
java -jar trimmomatic-0.40.jar SE \
  -threads 2 \
  input.fq \
  output.fq \
  AVGQUAL:20 \
  MINLEN:50
```

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

### Single-End Trimming with Compression Control

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Performs single-end trimming with sliding window quality filtering and minimum length requirements, while controlling the compression level of the output file.

```bash
java -jar trimmomatic-0.40.jar SE \
  -threads 4 \
  -compressLevel 6 \
  -compressBlock \
  input.fastq.gz \
  output.fastq.gz \
  SLIDINGWINDOW:4:20 MINLEN:36
```

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

### Minlen and Maxlen Length Filtering

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Filters reads based on minimum (MINLEN) or maximum (MAXLEN) length thresholds. Reads outside the specified range are dropped.

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  MINLEN:36
```

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  MAXLEN:150
```

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  SLIDINGWINDOW:4:15 \
  MINLEN:50 \
  MAXLEN:150
```

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

### Sliding Window Quality Trimming (Aggressive)

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Performs more aggressive sliding window quality trimming on single-end reads. Uses a 5-base window and a quality threshold of 20.

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  SLIDINGWINDOW:5:20
```

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

### Tophred33 and Tophred64 Quality Conversion

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Converts quality scores between Phred-33 and Phred-64 encodings. Use the -phred64 flag when input is Phred-64 encoded.

```bash
java -jar trimmomatic-0.40.jar SE \
  -phred64 \
  input_phred64.fq.gz output_phred33.fq.gz \
  TOPHRED33
```

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

### Paired-End Trimming with Read Pair Validation

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Enables read pair validation during paired-end trimming, ensuring that only valid pairs are processed. The '-quiet' flag suppresses verbose output.

```bash
java -jar trimmomatic-0.40.jar PE \
  -threads 4 \
  -validatePairs \
  -quiet \
  input_forward.fq.gz input_reverse.fq.gz \
  out_1P.fq.gz out_1U.fq.gz out_2P.fq.gz out_2U.fq.gz \
  ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 \
  LEADING:3 TRAILING:3 MINLEN:36
```

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

### Avgqual Average Quality Filtering

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Drops entire reads if their average quality score falls below a specified threshold. Can be combined with other trimming steps.

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  AVGQUAL:20
```

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  AVGQUAL:30 \
  MINLEN:50
```

```bash
java -jar trimmomatic-0.40.jar PE \
  input_R1.fq.gz input_R2.fq.gz \
  out_1P.fq.gz out_1U.fq.gz out_2P.fq.gz out_2U.fq.gz \
  ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 \
  SLIDINGWINDOW:4:15 \
  AVGQUAL:25 \
  MINLEN:36
```

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

### Basecount Base Filtering

Source: https://context7.com/usadellab/trimmomatic/llms.txt

Filters reads based on the count of specific bases, such as N (ambiguous calls) or GC content. Specify minimum and maximum counts for filtering.

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  BASECOUNT:N:0:5
```

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  BASECOUNT:GC:20:80
```

```bash
java -jar trimmomatic-0.40.jar SE \
  input.fq.gz output.fq.gz \
  BASECOUNT:N:0:0
```

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