Trimmomatic
A flexible trimmer for Illumina sequence data
Dados Bibliográficos
| ID | 23329985 |
|---|---|
| Autores | Anthony M Bolger (Forschungszentrum Jülich), Anthony Bolger (Forschungszentrum Jülich), Marc Lohse (0009-0005-7498-7279, Forschungszentrum Jülich), Bjoern Usadel (Forschungszentrum Jülich), Björn Usadel (0000-0003-0921-8041, Forschungszentrum Jülich, autor correspondente) |
| Ano | 2014 |
| Volume | 30 |
| Fascículo | 15 |
| Páginas | 2114-2120 |
| Data de publicação | 2014-08-01 |
| Peer Reviewed | Sim |
| Open Access | Sim |
| Tipo | ARTICLE |
| Periódico | Bioinformatics (JOURNAL) |
| Identificadores do periódico | ISSN: 1367-4803 • E-ISSN: 1367-4811 |
| Editora | Oxford University Press (OUP) (PUBLISHER) |
| DOI | 10.1093/bioinformatics/btu170 |
| PMID | 24695404 |
| PMCID | PMC4103590 |
| OpenAlex | W2131271579 |
| Idioma | EN |
| Citações recebidas | 112 |
| Referências citadas | 10 |
Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.
Biology · Data mining · Data pre-processing · Flexibility (engineering) · Java · Operating system · Preprocessor · Programming language · Sequence (biology) · Computer Science · Genetics, Bioinformatics, and Biomedical Research · Genomics and Phylogenetic Studies · Genomics and Rare Diseases
Comparison of crude-oil induced cardiotoxicity between Pacific herring stocks
No evidence for mitochondrial genetic variability in the largest population of critically endangered Tonkin snub-nosed monkeys in Vietnam
Cultivation, chemistry, and genome of Psilocybe zapotecorum
Resistoma y genómica comparativa de aislados clínicos de Escherichia coli diarreogénica en Lima, Perú
Dysrhythmic saliva microbiota in mobile phone addicts with sleep disorders and restored by acupuncture
Genetic and Phenotypic Evidence Reveals a Complex Evolutionary History within the Amazonian Allobates juami/insperatus Clade (Anura, Aromobatidae), with the Description of a New Species
A traveling Sars-CoV-2 laboratory as part of a pandemic response among vulnerable Brazilian populations
Metagenomic and genomic characterization of heavy metal tolerance and resistance genes in the rhizosphere microbiome of Avicennia germinans in a semi-arid mangrove forest in the tropics
A new coronavirus associated with human respiratory disease in China
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Dendritic Spine in Autism Genetics
Intron retention as an excellent marker for diagnosing depression and for discovering new potential pathways for drug intervention
DNA Methylation in Healthy Older Adults With a History of Childhood Adversity—Findings From the Women 40+ Healthy Aging Study
The Genomic Landscape of a Restricted ALL Cohort from Patients Residing on the U.S./Mexico Border
Anti-Biofouling Performance of an Immobilized Indigenous Quorum Quenching Bacterium Bacillus cereus HG10 and Its Influence on the Microbial Community in a Bioreactor
A Preliminary Study of Bacterioplankton Community Structure in the Taiyangshan Wetland in Ningxia and Its Driving Factors
High Frequency of Antibiotic Resistance Genes (ARGs) in the Lerma River Basin, Mexico
Identification and Genetic Characterization of Mers-Related Coronavirus Isolated from Nathusius’ Pipistrelle (Pipistrellus nathusii) near Zvenigorod (Moscow Region, Russia)
Effects of Elevation and Distance from Highway on the Abundance and Community Structure of Bacteria in Soil along Qinghai-Tibet Highway
Effects of Pb Smelting on the Soil Bacterial Community near a Secondary Lead Plant
Changes in the Composition of the Soil Bacterial Community in Heavy Metal-Contaminated Farmland
Carbon dioxide fertilization effect on rice yield is not sustained over multiple generations
Lethal Outcome of Leptospirosis in Southern Russia
Differential H3K9me2 heterochromatin levels and concordant mRNA expression in postmortem brain tissue of individuals with schizophrenia, bipolar, and controls
Serratia marcescens Outbreak at a Correctional Facility
Whole Transcriptome Sequencing of Peripheral Blood Shows That Immunity/GnRH/PI3K-Akt Pathways Are Associated With Opioid Use Disorder
Gut Microbiome Composition Associated With Major Depressive Disorder and Sleep Quality
Transcriptome Changes in Relation to Manic Episode
Microbiome of Unilateral Chronic Rhinosinusitis
Genetic Diversity of Antimicrobial Resistance and Key Virulence Features in Two Extensively Drug-Resistant Acinetobacter baumannii Isolates
Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis
Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation
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Whole-genome sequencing-based genetic diversity, transmission dynamics, and drug-resistant mutations in Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia
Antimicrobial resistance and genomic investigation of non-typhoidal Salmonella isolated from outpatients in Shaoxing city, China
Whole genome sequencing of neurotoxin-producing Clostridium species in New York state to bolster epidemiological investigations and reveal patterns of diversity and distribution
Circulation of ESBL-producing Klebsiella pneumoniae at the human–animal–environment interface in farms on the central coast of Peru
Traceability analysis of a foodborne disease outbreak caused by Clostridium perfringens in Ma’anshan City, Anhui Province, 2024
Irida-Aries Genomics, a key player in the One Health surveillance of diseases caused by infectious agents in Italy
Genomic evolution of BA.5.2 and BF.7.14 derived lineages causing Sars-CoV-2 outbreak at the end of 2022 in China
Repeat infections with chlamydia in women may be more transcriptionally active with lower responses from some immune genes
Investigation of invasive Neisseria meningitidis serogroup Y ST1466 case increases in New York State
High diversity of clinical Mycobacterium intracellulare in China revealed by whole genome sequencing
Genomic surveillance during the first two years of the Covid-19 pandemic – country experience and lessons learned from Türkiye
Genotypes and drug resistance pattern of Mycobacterium tuberculosis complex among clinically diagnosed pulmonary tuberculosis patients
Integrative analysis of RNA-sequencing and microarray for the identification of adverse effects of UVB exposure on human skin
The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada
Association of intestinal microbiota markers and dietary pattern in Chinese patients with type 2 diabetes
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Analysis of metatranscriptomic methods to enable wastewater-based biosurveillance of all infectious diseases
Short- and long-term effects of radiation exposure at low dose and low dose rate in normal human VH10 fibroblasts
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Combined Effects of Proton Radiation and Simulated Microgravity on the Cell Viability and ALP Activity of Murine Osteoblast Cells
Empowering tuberculosis genomic surveillance in Limpopo, South Africa through capacity building
Surveillance of tick-borne bacteria infection in ticks and forestry populations in Inner Mongolia, China
Population Structure of Listeria monocytogenes in Emilia-Romagna (Italy) and Implications on Whole Genome Sequencing Surveillance of Listeriosis
Differential transcriptome profile underlying risky choice in a rat gambling task
Rapid, but limited, zooplankton adaptation to simultaneous warming and acidification
Microbial functional genes within soil aggregates drive organic carbon mineralization under contrasting tillage practices
Soil bacterial community and ecosystem multifunctionality regulated by keystone plant species during secondary succession
Linking microbial community structure to function underneath moss‐dominated biocrusts in rare earth elements mine areas under a subtropical climate
Bacterial communities in proso millet root‐associated compartments are regulated by growth period and mulching regime
Pathways and Risks of Antibiotic Resistance Genes Along a Rural to Urban River Gradient
The incorporation of straw into the subsoil increases C, N, and P enzyme activities and nutrient supply by enriching distinctive functional microorganisms
Soil bacterial and fungal communities and associated nutrient cycling in relation to rice cultivation history after reclamation of natural wetland
Salt‐tolerant broomcorn millet ( Panicum miliaceum L.) resists salt stress via modulation of cell wall biosynthesis and Na + balance
Paeonia lactiflora Pall. Polysaccharide alleviates depression in Cums mice by inhibiting the NLRP3/ASC/Caspase-1 signaling pathway and affecting the composition of their intestinal flora
Jianghu decoction and its active component polydatin inhibit inflammation and fibrotic lesions in the lungs of ILD mice via the AMPK signaling pathway
MC1R diversity and its role in skin pigmentation variation in West Maharashtra, India
Consequences of integrating livestock and wildlife in an African savanna
Enzyme morphinan N-demethylase for more sustainable opiate processing
Analytic optimization of Plasmodium falciparum marker gene haplotype recovery from amplicon deep sequencing of complex mixtures
Metagenomic next-generation sequencing to characterize potential etiologies of non-malarial fever in a cohort living in a high malaria burden area of Uganda
First detection of one of the tick-borne lymphadenopathy (Tibola) etiological agent in ticks from a highly frequented sub-urban forest near Paris, France
Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing
Plasmodium falciparum importation does not sustain malaria transmission in a semi-arid region of Kenya
Respiratory virus infection dynamics and genomic surveillance to detect seasonal influenza subtypes in wastewater
Near-term pregnant women in the Dominican Republic experience high rates of Group B Streptococcus rectovaginal colonization with virulent strains
Fungal community and functional responses to soil warming are greater than for soil nitrogen enrichment
Heavy Rainfall, Sewer Overflows, and Salmonellosis in Black Skimmers (Rynchops niger)
Different Roles of Wild Boars and Livestock in Salmonella Transmission to Humans in Italy
Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies
Precursors to the 1918 pandemic
The development and ecology of the Japanese macaque gut microbiome from weaning to early adolescence in association with diet
Unveiling the Evolutionary History of c is‐ Andean Alouatta (Atelidae, Alouattinae) Through Mitochondrial Genomes
Divergence in gut microbial communities mirrors a social group fission event in a black‐and‐white colobus monkey ( Colobus vellerosus )
Season, age, and sex affect the fecal mycobiota of free‐ranging Tibetan macaques ( Macaca thibetana )
Revised Evolutionary and Taxonomic Synthesis for Parrots (Order
Fourteen New, Endemic Species of Shrew (Genus Crocidura) from Sulawesi Reveal a Spectacular Island Radiation
Phosphate‐Solubilizing Bacteria Enhance Carbon Accumulation by Mediating Microbial Functions in Alpine Restoration
Microbial-based separate and simultaneous saccharification and ethanol fermentation of poplar (Populus euramericana) substrate
The pharmacological validation of the Xiao-Jian-Zhong formula against ulcerative colitis by network pharmacology integrated with metabolomics
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The protective role of Achyranthes aspera extract against cisplatin-induced nephrotoxicity by alleviating oxidative stress, inflammation, and PANoptosis
Health risk of Licorice-Yuanhua combination through induction of colonic H2S metabolism
| Obras citantes distintas | 112 |
|---|---|
| Citações por ano | 11,2 |
| Intervalo de citações | 2016 - 2026 (11) |
| Velocidade de citação | current |
| Altamente citado | Sim |
| Tipos de citação | Neutras: 106 |