Trimmomatic

http://www.usadellab.org/cms/?page=trimmomatic
Admin
Trimmomatic is a flexible read trimming tool for Illumina NGS data that performs adapter clipping,...
Tokens:2,575
Snippets:40
Trust Score:5.5
Update:6 months ago
Show doc for...
Tokens:
Raw
### LEADING Step

Source: http://www.usadellab.org/cms/?page=trimmomatic

Removes low-quality bases from the start of reads. Requires the minimum quality threshold.

```bash
LEADING:<quality>
```

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

### CROP Step

Source: http://www.usadellab.org/cms/?page=trimmomatic

Trims reads to a specific length from the start. Requires the desired length.

```bash
CROP:<length>
```

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

### HEADCROP Step

Source: http://www.usadellab.org/cms/?page=trimmomatic

Removes a specified number of bases from the start of reads. Requires the number of bases to remove.

```bash
HEADCROP:<length>
```

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

### SLIDINGWINDOW Step

Source: http://www.usadellab.org/cms/?page=trimmomatic

Trims bases based on a sliding window average quality. Requires window size and minimum average quality.

```bash
SLIDINGWINDOW:<windowSize>:<requiredQuality>
```

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

### ILLUMINACLIP Step

Source: http://www.usadellab.org/cms/?page=trimmomatic

Removes adapter sequences. Requires a FASTA file containing adapter sequences, seed mismatch count, palindrome clip threshold, and simple clip threshold.

```bash
ILLUMINACLIP:<fastaWithAdaptersEtc>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold>
```

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

### MINLEN Step

Source: http://www.usadellab.org/cms/?page=trimmomatic

Filters out reads shorter than a specified minimum length. Requires the minimum length.

```bash
MINLEN:<length>
```

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

### Run Trimmomatic for Single-End Data

Source: http://www.usadellab.org/cms/?page=trimmomatic

Executes Trimmomatic in single-end mode using the specified adapter file and quality thresholds.

```bash
java -jar trimmomatic-0.35.jar SE -phred33 input.fq.gz output.fq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
```

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

### Run Trimmomatic for Paired-End Data

Source: http://www.usadellab.org/cms/?page=trimmomatic

Executes Trimmomatic in paired-end mode with specific quality trimming and adapter clipping parameters.

```bash
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
```

```bash
java -jar trimmomatic-0.35.jar PE -phred33 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
```

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

### Paired End Mode Command

Source: http://www.usadellab.org/cms/?page=trimmomatic

Use this command for processing paired-end sequencing data. Specify the path to the Trimmomatic JAR, input files, output files, and any trimming steps.

```bash
java -jar <path to trimmomatic.jar> PE [-threads <threads] [-phred33 | -phred64] [-trimlog <logFile>] <input 1> <input 2> <paired output 1> <unpaired output 1> <paired output 2> <unpaired output 2> <step 1> ...
```

```bash
java -classpath <path to trimmomatic jar> org.usadellab.trimmomatic.TrimmomaticPE [-threads <threads>] [-phred33 | -phred64] [-trimlog <logFile>] <input 1> <input 2> <paired output 1> <unpaired output 1> <paired output 2> <unpaired output 2> <step 1> ...
```

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

### Single End Mode Command

Source: http://www.usadellab.org/cms/?page=trimmomatic

Use this command for processing single-end sequencing data. Specify the path to the Trimmomatic JAR, input file, output file, and any trimming steps.

```bash
java -jar <path to trimmomatic jar> SE [-threads <threads>] [-phred33 | -phred64] [-trimlog <logFile>] <input> <output> <step 1> ...
```

```bash
java -classpath <path to trimmomatic jar> org.usadellab.trimmomatic.TrimmomaticSE [-threads <threads>] [-phred33 | -phred64] [-trimlog <logFile>] <input> <output> <step 1> ...
```

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

### Single End Mode

Source: http://www.usadellab.org/cms/?page=trimmomatic

Executes Trimmomatic in single-end mode to process a single input file.

```APIDOC
## CLI: Single End Mode

### Description
Processes single-end sequencing data using one input file and generating one output file.

### Parameters
- **threads** (int) - Optional - Number of threads to use.
- **phred33/phred64** (flag) - Optional - Quality score encoding (default is phred64).
- **trimlog** (file) - Optional - Path to log file for read trimming details.
- **input** (file) - Required - Input FASTQ file.
- **output** (file) - Required - Output FASTQ file.
- **steps** (list) - Required - Trimming steps to apply.
```

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

### TRAILING Step

Source: http://www.usadellab.org/cms/?page=trimmomatic

Removes low-quality bases from the end of reads. Requires the minimum quality threshold.

```bash
TRAILING:<quality>
```

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

### Paired End Mode

Source: http://www.usadellab.org/cms/?page=trimmomatic

Executes Trimmomatic in paired-end mode to process two input files and generate paired and unpaired output files.

```APIDOC
## CLI: Paired End Mode

### Description
Processes paired-end sequencing data using two input files and generating four output files (paired/unpaired for each input).

### Parameters
- **threads** (int) - Optional - Number of threads to use.
- **phred33/phred64** (flag) - Optional - Quality score encoding (default is phred64).
- **trimlog** (file) - Optional - Path to log file for read trimming details.
- **input 1** (file) - Required - First input FASTQ file.
- **input 2** (file) - Required - Second input FASTQ file.
- **paired output 1** (file) - Required - Output for surviving paired reads from input 1.
- **unpaired output 1** (file) - Required - Output for unpaired reads from input 1.
- **paired output 2** (file) - Required - Output for surviving paired reads from input 2.
- **unpaired output 2** (file) - Required - Output for unpaired reads from input 2.
- **steps** (list) - Required - Trimming steps to apply.
```
Tokens:
Raw