Trimmomatic pipeline

Trimmomatic specifications


Unique identifier OMICS_01097
Name Trimmomatic
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTQ
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.36
Stability Stable
Source code URL
Maintained Yes



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  • person_outline Anthony Bolger <>

Publication for Trimmomatic

Trimmomatic IN pipelines

PMCID: 5739345
PMID: 29091815
DOI: 10.1016/j.phytochem.2017.10.004

[…] reads. read quality was assessed using fastqc (v0.11.2; with default parameters and adaptors and low quality sequences removed using trimmomatic (parameter: leading:10 trailing:10 slidingwindow:4:15 minlen:30) (v0.32, (bolger et al., 2014). only surviving paired-end reads were used to generate de novo assemblies using trinity […]

PMCID: 5754050
PMID: 29300724
DOI: 10.1371/journal.pgen.1007127

[…] (illumina). all fastq files corresponding to the same sample (derived from separately sequenced lanes) were then merged into a single fastq file (one per sample). read trimming was performed with trimmomatic (v0.36) with the following settings “crop:75 headcrop:5 slidingwindow:20:20 minlen:36”. the mouse reference genome grcm38 (version m12, ensembl release 87) and the ercc reference sequence […]

PMCID: 5754486
PMID: 29301877
DOI: 10.1128/genomeA.01391-17

[…] and genome libraries were constructed using a truseq dna pcr-free library preparation kit (illumina, inc.). the quality of the raw data was checked with fastqc (8), and adapters were trimmed with trimmomatic (9). the genomes were assembled with velvet version 1.2.10 (10) and annotated with the ncbi prokaryotic genome annotation pipeline (11)., the ehec strain eca1 and epec strain ecb1 draft […]

PMCID: 5756330
PMID: 29304737
DOI: 10.1186/s12864-017-4415-x

[…] using high-quality illumina and long nanopore reads [10]. non-specific matches were mapped randomly., abundance of transcripts were determined by mapping quality-filtered and adapter-trimmed reads (trimmomatic v0.36) to the published reference genome of g. oxydans using bowtie2 v2.2.7 [41, 42]. cufflinks and cuffnorm were used to quantify transcript levels [43]., detection of tsss was done […]

PMCID: 5758643
PMID: 29311719
DOI: 10.1038/s41598-017-18445-0

[…] hiseq 2000 sequencing yielded single-read sequences with length of 100 bp. the quality of the reads was checked using fastqc (v. 0.11.3) and overall quality was improved by trimming the reads using trimmomatic121, with following parameters: crop = 95, headcrop = 10, minlen = 85., high quality rna-seq reads were mapped using the clc genomics workbench (v. 9.5.3)., traces of ribosomal rna […]

Trimmomatic institution(s)
Department Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Golm,Institut für Biologie I, RWTH Aachen, Aachen and Institute of Bio- and Geosciences: Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
Trimmomatic funding source(s)
Supported by the BMBF through grants 0315702F, 0315961 and 0315049A and BLE/BMELV Verbundprojekt: G 127/10 IF.

Trimmomatic review

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Arup Ghosh

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A great tool for raw sequence file manipulation. Trimmomatic offers various quality control filters for raw sequenced reads, also the tool is compatible with paired-end sequencing data.