### 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: ``` -------------------------------- ### 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: ``` -------------------------------- ### 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: ``` -------------------------------- ### 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:: ``` -------------------------------- ### 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:::: ``` -------------------------------- ### 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: ``` -------------------------------- ### 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 PE [-threads ] ... ``` ```bash java -classpath org.usadellab.trimmomatic.TrimmomaticPE [-threads ] [-phred33 | -phred64] [-trimlog ] ... ``` -------------------------------- ### 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 SE [-threads ] [-phred33 | -phred64] [-trimlog ] ... ``` ```bash java -classpath org.usadellab.trimmomatic.TrimmomaticSE [-threads ] [-phred33 | -phred64] [-trimlog ] ... ``` -------------------------------- ### 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: ``` -------------------------------- ### 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. ``` === COMPLETE CONTENT === This response contains all available snippets from this library. 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