LEADING: Cut bases off the start of a read, if below a threshold quality.SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold.ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. This will perform the same steps, using the single-ended adapter file 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 Drop reads below the 36 bases long (MINLEN:36).Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15).Remove trailing low quality or N bases (below quality 3) (TRAILING:3).Remove leading low quality or N bases (below quality 3) (LEADING:3).Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10).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 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:keepBothReads LEADING:3 TRAILING:3 MINLEN:36įor reference only (less sensitive for adapters) RNAseq expression analysis vs DNA assembly). If you have questions please don't hesitate to contact us, this is not necessarily one size fits all. Note the additional :2 in front of keepBothReads this is the minimum adapter length in palindrome mode, you can even set this to 1. Also in general keepBothReads can be useful when working with paired end data, you will keep even redunfant information but this likely makes your pipelines more manageable. You often don't need leading and traling clipping. With most new data sets you can use gentle quality trimming and adapter clipping. Version 0.36: binary and source Quick start Paired End: Starting on version 0.40 we also offer a github page (as well as older versions) Trimmomatic: A flexible trimmer for Illumina Sequence Data. Trimmomatic: A flexible read trimming tool for Illumina NGS dataīolger, A.

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