It can be compressed ( or foo.fq.gz) or uncompressed (foo.fq or foo.fastq). input_ is your input file for read 1 (R1, typically something like XXX_S1_R1.fastq.gz).PE indicates the sequencing was paired end (PE).

Java -jar /whereIsTrimmomatic /trimmomatic - 0.36.jar PE input_ input_ output_forward_ output_forward_ output_reverse_ output_reverse_ ILLUMINACLIP :NexteraPE -PE.fa : 2 : 30 : 10 LEADING : 3 TRAILING : 3 SLIDINGWINDOW : 4 : 15 MINLEN : 36 You may however want to adapt according to your project’s specificity or requirements. I usually use the settings present in this command line. MINLEN:32 is the minimum length of trimmed/controled reads (here 32).SLIDINGWINDOW:4:15 Trimmomatic scans the reads in a 4 base window… If mean quality drops under 15, the read is trimmed.TRAILING:3 is the quality under which trailing (hence the last, at the end of the read) nucleotide is trimmed.LEADING:3 is the quality under which leading (hence the first, at the beginning of the read) nucleotide is trimmed.:2:30:10 are mismatch/accuracy treshold for adapter/reads pairing.Beware, Nextera adapters (works for Nextera XT too) are always PE adapters (can be used for PE and SE). You may have to specify the path to it in certain conditions. NexteraPE-PE is the fasta file’s name that contain the adapters sequence (given with the program you could also add your custom ones).SE indicates the sequencing was single end (SE)./whereIsTrimmomatic/trimmomatic-0.36.jar is the path to the program.java -jar calls the Java interpreter, as Trimmomatic is coded in Java.Let’s have a look on all the arguments of this command: Java -jar /whereIsTrimmomatic /trimmomatic - 0.36.jar SE ILLUMINACLIP :NexteraPE -PE : 2 : 30 : 10 LEADING : 3 TRAILING : 3 SLIDINGWINDOW : 4 : 15 MINLEN : 32

Trimmomatic crop example