Trimmomatic protocols

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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 0.38
Stability Stable
Source code URL
Maintained Yes



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  • person_outline Anthony Bolger <>

Publication for Trimmomatic

Trimmomatic in pipelines

PMCID: 5752201
PMID: 29297464
DOI: 10.7554/eLife.29815.043

[…] (from three biological replicates) were sequenced., rna-seq libraries were sequenced on illumina hiseq2000 with single read to 50 bp. we clipped adapters and trimmed low quality bases using trimmomatic version 0.30 (rrid:scr_011848) () with parameters ‘se –s phred33 illuminaclip:illumina_smallrna_adapters.fa:1:20:5 leading:30 trailing:30 minlen:10’, where illumina_smallrna_adapters.fa […]

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: 5754362
PMID: 29302059
DOI: 10.1038/s41467-017-02512-1

[…] reads per lane, and using a single-read 100-cycle protocol. the data were analyzed as outlined above for rna-seq., to study chromatin transitions by chip-seq analysis, sequences were filtered using trimmomatic and mapped to the rn6 reference rat genome using the bowtie2 aligner as described above (rna-seq data analysis). to identify the regions of the genome enriched in h3k27ac and h3k4me1, […]

PMCID: 5754480
PMID: 29301900
DOI: 10.1128/genomeA.01292-17

[…] per infected cell., the apc_jm3.2 phage genome was sequenced by using illumina miseq technology (teagasc food research centre, moorepark, fermoy, co. cork). reads were trimmed and filtered by using trimmomatic () to remove adaptor sequences and reads less than 70 bp when a sliding window of 4 bp and minimum phred score of 30 was applied. subsequent read quality was assessed using fastqc […]

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

[…]  bp, 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 (), and adapters were trimmed with trimmomatic (). the genomes were assembled with velvet version 1.2.10 () and annotated with the ncbi prokaryotic genome annotation pipeline ()., the ehec strain eca1 and epec strain ecb1 draft genomes […]

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Trimmomatic in publications

PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z

[…] expression in the medial basal hypothalamus during pubertal development was determined by employing the edger analysis package. an initial trimming and adaptor removal step was carried out using trimmomatic. removal of the illumina adapter sequences and default filtering parameters was performed as suggested in the program’s documentation, with exception of a hard clip of the first 13 bases […]

PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] paired-end sequencing on an illumina hiseq3000., to process demultiplexed raw reads for phylogenomic analyses, we followed the standard phyluce pipeline (). illumiprocessor, in combination with trimmomatic, was used to filter low-quality reads and remove adapters (, ), yielding an average of 8,504,473 reads (302,468 to 119,426,985) and 1,141,548,626 bp (42,543,058 to 17,007,264,440) per […]

PMCID: 5954203
DOI: 10.1128/mSystems.00205-17

[…] instrument (paired end)., see for an overview of the data analysis steps. briefly, quality control (qc) of mirna sequencing data was performed using fastqc before and after adaptor trimming with trimmomatic (). then, the paired-end reads were assembled using pandaseq and aligned to the hg38 genome assembly using bowtie2 (, ). finally, the total mature mirna counts were generated with htseq […]

PMCID: 5954019
PMID: 29765032
DOI: 10.1038/s41467-018-03781-0

[…] dna libraries were sequenced and the raw reads were processed with the protocols adopted in previous study. briefly, the adapter and low quality sequences were trimmed from 3′ to 5′ ends by trimmomatic. after trimming, reads shorter than 36 bp were discarded. subsequently, the preprocessed reads were aligned to mouse reference genome (mm9) using bowtie2. then, the aligned reads […]

PMCID: 5952695
PMID: 29764377
DOI: 10.1186/s12864-018-4756-0

[…] fed with a diet sprayed with 95% ethanol containing fadrozole (sigma) at a concentration of 200 μg/g diet for 45 (45 dat) and 90 days (90 dat)., after trimming adapters and low quality sequence with trimmomatic [], the clean reads were aligned to a tilapia reference genome assembly [] using tophat [], allowing up to 2 base mismatches per read. ncbi refseq annotations were used to guide […]

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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 reviews

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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.


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Excellent tool for trimming fastq files from Illumina for several NGS applications.