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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




No version available



  • person_outline Anthony Bolger

Publication for Trimmomatic

Trimmomatic citations


Elucidating the genetic architecture of reproductive ageing in the Japanese population

Nat Commun
PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z
call_split See protocol

[…] gene 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 o […]


Multiple origins of green blood in New Guinea lizards

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

[…] 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 samp […]


Comparative whole genome re sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

PMCID: 5953909
PMID: 29766351
DOI: 10.1186/s12284-018-0224-3

[…] ic DNA (ranging from approx. 0.2 to 10 kb) using TruSeq DNA PCR-FREE (350 bp) (Illumina), and 101 bp paired-end short reads were generated in fastq format. The obtained raw data were processed by the Trimmomatic software version 0.33 (Bolger et al. ) with the options of ‘LEADING:15, TRAINLING:15, SLIDINGWINDOW:4:15, MINLEN:20’ to trim adapter and low-quality sequences. The raw sequencing data were […]


Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

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

[…] 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 () […]


PCGF5 is required for neural differentiation of embryonic stem cells

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

[…] llumina). 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 were conv […]


Transcriptome display during tilapia sex determination and differentiation as revealed by RNA Seq analysis

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

[…] 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 the Cuffli […]


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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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Anonymous user #21610

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