NextFlow statistics

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Citations per year

Number of citations per year for the bioinformatics software tool NextFlow

Tool usage distribution map

This map represents all the scientific publications referring to NextFlow per scientific context
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Associated diseases

This word cloud represents NextFlow usage per disease context

Popular tool citations

chevron_left Read alignment SNP detection SNV detection File indexation Workflow management systems Reference-based transcriptome assembly Nucleotide sequence homology search Indel detection chevron_right
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NextFlow specifications


Unique identifier OMICS_25663
Name NextFlow
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Groovy, Java, Javascript, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.27.0-RC2
Stability Stable
High performance computing Yes
Maintained Yes




No version available



  • person_outline Cédric Notredame
  • person_outline NextFlow Team

Additional information

Publication for NextFlow

NextFlow citations


Transposable Element Genomic Fissuring in Pyrenophora teres Is Associated With Genome Expansion and Dynamics of Host–Pathogen Genetic Interactions

Front Genet
PMCID: 5915480
PMID: 29720997
DOI: 10.3389/fgene.2018.00130

[…] were identified using the MAKER recommended method (). To ensure comparability of results between assemblies and reproducibility of results more generally, the method was formalized as a reproducible Nextflow pipeline (). The pipeline is available at terminal repeat (LTR) elements were detected using two parallel runs of the LTR harvest () and LTRdigest ( […]


Discovery of genomic intervals that underlie nematode responses to benzimidazoles

PLoS Negl Trop Dis
PMCID: 5895046
PMID: 29601575
DOI: 10.1371/journal.pntd.0006368

[…] raw and TPM (transcripts per million) read counts for annotated genes, respectively. DESeq2 [] was used to identify differentially expressed genes. The complete RNA-seq pipeline was implemented with Nextflow [] and is publicly available through GitHub ( […]


Ten steps to get started in Genome Assembly and Annotation

PMCID: 5850084
PMID: 29568489
DOI: 10.5256/f1000research.14771.r31487

[…] ile being hosted on a different host environment. Once encapsulated this way, analysis pipelines were shown to become entirely repeatable across platforms.Several workflow management systems, such as Nextflow, Toll and Galaxy, have recently been reported as having the capacity to use and deploy containers. These tools all share the same philosophy: they make it relatively easy to define and implem […]


R Spondin chromosome rearrangements drive Wnt dependent tumour initiation and maintenance in the intestine

Nat Commun
PMCID: 5508203
PMID: 28695896
DOI: 10.1038/ncomms15945
call_split See protocol

[…] to convert mouse gene symbols to human gene symbols. We used DESeq2 to perform all differential expression analyses (v1.12.3), and utilized Nextflow ( to implement our computational pipelines. […]


Enhancing knowledge discovery from cancer genomics data with Galaxy

PMCID: 5437943
PMID: 28327945
DOI: 10.1093/gigascience/gix015

[…] se issues produce a tremendous barrier for new users.There exist a handful of options that address this predicament in genomics as a whole. Tools that automate pipeline development such as Kronos [], Nextflow [], and Snakemake [] can satisfy the needs of more technically savvy users. Alternatively, graphical user interfaces (GUIs)—which are generally lacking in the field of bioinformatics—aid in u […]


The growing need for microservices in bioinformatics

J Pathol Inform
PMCID: 5139451
PMID: 27994937
DOI: 10.4103/2153-3539.194835

[…] The concepts found in the core on-line Docker documentation can be applied broadly, but such information is also helpful in support of bioinformatics projects that might make use of the Docker model. NextFlow,[] the PanCancer Launcher[] from the International Cancer Genome Consoritum, and BaseSpace[] from Illumina, are a few examples of contemporary tools that take advantage of Docker to help mana […]

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NextFlow institution(s)
Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
NextFlow funding source(s)
Supported by the Center for Genomic Regulation and the Spanish Plan Nacional and the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’, La Caixa Foundation, and the CERCA Programme/Generalitat de Catalunya.

NextFlow review

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When you'll learn how to use it, you'll love it:)