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ArticlesPeer ReviewedFull Text
Nextflow enables reproducible computational workflows
Author / Creator:Di Tommaso, Paolo ; Chatzou, Maria ; Floden, Evan W ; Barja, Pablo Prieto ; Palumbo, Emilio ; Notredame, Cedric
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2017-04, Vol.35 (4), p.316-319
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TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity
Author / Creator:Theaud, Guillaume ; Houde, Jean-Christophe ; Boré, Arnaud ; Rheault, François ; Morency, Felix ; Descoteaux, Maxime
Publisher:United States: Elsevier Inc
Journal title:NeuroImage (Orlando, Fla.), 2020-09, Vol.218, p.116889-116889, Article 116889
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scalepopgen: Bioinformatic Workflow Resources Implemented in Nextflow for Comprehensive Population Genomic Analyses
Author / Creator:Upadhyay, Maulik ; Pogorevc, Neža ; Medugorac, Ivica
Publisher:UK: Oxford University Press
Journal title:Molecular biology and evolution, 2024-04, Vol.41 (4)
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PGSXplorer: an integrated nextflow pipeline for comprehensive quality control and polygenic score model development
Author / Creator:Yaraş, Tutku ; Oktay, Yavuz ; Karakülah, Gökhan
Publisher:United States: PeerJ. Ltd
Journal title:PeerJ (San Francisco, CA), 2025-02, Vol.13, p.e18973
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GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data
Author / Creator:Liu, Xiaochuan ; Bienkowska, Jadwiga R. ; Zhong, Wenyan
Publisher:San Francisco: Public Library of Science
Journal title:PloS one, 2020-08, Vol.15 (8), p.e0232994-e0232994
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RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow
Author / Creator:Lataretu, Marie ; Hölzer, Martin
Publisher:Switzerland: MDPI AG
Journal title:Genes, 2020-12, Vol.11 (12), p.1487
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MultiOmicsIntegrator: a nextflow pipeline for integrated omics analyses
Author / Creator:Pasat, Bianka Alexandra ; Pilalis, Eleftherios ; Mnich, Katarzyna ; Samali, Afshin ; Chatziioannou, Aristotelis ; Gorman, Adrienne M
Publisher:England: Oxford University Press
Journal title:Bioinformatics advances, 2024, Vol.4 (1), p.vbae175
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SpaFlow: a Nextflow pipeline for QC and clustering of MxIF datasets
Author / Creator:Novotny, Brenna C ; Moore, Raymond ; Langit, Lynn ; Haley, David ; Maus, Rachel L ; Jiang, Jun ; Ward, Caitlin ; Guo, Ray ; Goode, Ellen L ; Markovic, Svetomir N ; Wang, Chen
Publisher:England: Oxford University Press
Journal title:Bioinformatics advances, 2025, Vol.5 (1), p.vbaf032
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BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization
Author / Creator:Marchment, George ; Brancotte, Bryan ; Schmit, Marie ; Lemoine, Frédéric ; Cohen-Boulakia, Sarah
Publisher:England: Oxford University Press
Journal title:NAR genomics and bioinformatics, 2024-09, Vol.6 (3), p.lqae092
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eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts
Author / Creator:Chitneedi, Praveen Krishna ; Hadlich, Frieder ; Moreira, Gabriel C M ; Espinosa-Carrasco, Jose ; Li, Changxi ; Plastow, Graham ; Fischer, Daniel ; Charlier, Carole ; Rocha, Dominique ; Chamberlain, Amanda J ; Kuehn, Christa
Publisher:England: Oxford University Press
Journal title:NAR genomics and bioinformatics, 2024-09, Vol.6 (3), p.lqae122
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bcRflow: a Nextflow pipeline for characterizing B cell receptor repertoires from non-targeted transcriptomic data
Author / Creator:Schlegel, Brent T ; Morikone, Michael ; Mu, Fangping ; Tang, Wan-Yee ; Kohanbash, Gary ; Rajasundaram, Dhivyaa
Publisher:England: Oxford University Press
Journal title:NAR genomics and bioinformatics, 2024-09, Vol.6 (4), p.lqae137
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ArticlesPeer ReviewedFull Text
FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow
Author / Creator:Vlasova, Anna ; Hermoso Pulido, Toni ; Camara, Francisco ; Ponomarenko, Julia ; Guigó, Roderic
Publisher:Switzerland: MDPI AG
Journal title:Genes, 2021-10, Vol.12 (10), p.1645
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ArticlesPeer ReviewedFull Text
Nextflow vs. plain bash: different approaches to the parallelization of SNP calling from the whole genome sequence data
Author / Creator:Sztuka, Marek ; Kotlarz, Krzysztof ; Mielczarek, Magda ; Hajduk, Piotr ; Liu, Jakub ; Szyda, Joanna
Publisher:England: Oxford University Press
Journal title:NAR genomics and bioinformatics, 2024-06, Vol.6 (2), p.lqae040-lqae040
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nf-rnaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data
Author / Creator:Mpangase, Phelelani T ; Frost, Jacqueline ; Tikly, Mohammed ; Ramsay, Michèle ; Hazelhurst, Scott
Publisher:Makhanda: South African Computer Society (SAICSIT)
Journal title:South African computer journal = Suid-Afrikaanse rekenaartydskrif, 2021-12, Vol.33 (2), p.1-16
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ArticlesPeer ReviewedFull Text
QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data
Author / Creator:Ssekagiri, Alfred ; Jjingo, Daudi ; Lujumba, Ibra ; Bbosa, Nicholas ; Bugembe, Daniel L ; Kateete, David P ; Jordan, I King ; Kaleebu, Pontiano ; Ssemwanga, Deogratius
Publisher:England: Oxford University Press
Journal title:Bioinformatics advances, 2022, Vol.2 (1), p.vbac089-vbac089
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ArticlesPeer ReviewedFull Text
Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG [version 1; peer review: awaiting peer review]
Author / Creator:Yepes-García, Jeferyd ; Falquet, Laurent
Publisher:F1000 Research Ltd
Journal title:F1000 research, 2024, Vol.13, p.640
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ArticlesFull Text
Using the Nextflow framework for reproducible in-silico omics analyses across clusters and clouds
Author / Creator:Paolo Di Tommaso ; Floden, Evan ; Chatzou, Maria ; Notredame, Cedric
Publisher:San Diego: PeerJ, Inc
Journal title:PeerJ preprints, 2017-02
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ArticlesFull Text
Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline
Author / Creator:Patel, Yash ; Zhu, Chenghao ; Yamaguchi, Takafumi N ; Wang, Nicholas ; Wiltsie, Nicholas ; Zeltser, Nicole ; Gonzalez, Alfredo ; Winata, Helena ; Pan, Yu ; Mohammen Faizal Eeman Mootor ; Sanders, Timothy ; Fitz-Gibbon, Sorel T ; Kandoth, Cyriac ; Livingstone, Julie ; Liu, Lydia Y ; Carlin, Benjamin ; Holmes, Aaron ; Oh, Jieun ; Sahrmann, John ; Shu Tao ; Eng, Stefan ; Hugh-White, Rupert ; Pashminehazar, Kiarod ; Park, Andrew ; Beshlikyan, Arpi ; Madison, Jordan ; Wu, Selina ; Mao Tian ; Arbet, Jaron ; Neilsen, Beth ; Haas, Roni ; Yuan Zhe Bugh ; Kim, Gina ; Salmingo, Joseph ; Zhang, Wenshu ; Aakarsh Anand ; Hwang, Edward ; Neiman-Golden, Anna ; Steinberg, Philippa ; Zhao, Wenyan ; Anand, Prateek ; Agrawal, Raag ; Tsai, Brandon L ; Boutros, Paul C
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2025-03
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Enhanced protein isoform characterization through long-read proteogenomics
Author / Creator:Miller, Rachel M. ; Jordan, Ben T. ; Mehlferber, Madison M. ; Jeffery, Erin D. ; Chatzipantsiou, Christina ; Kaur, Simi ; Millikin, Robert J. ; Dai, Yunxiang ; Tiberi, Simone ; Castaldi, Peter J. ; Shortreed, Michael R. ; Luckey, Chance John ; Conesa, Ana ; Smith, Lloyd M. ; Deslattes Mays, Anne ; Sheynkman, Gloria M.
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2022-03, Vol.23 (1), p.69-69, Article 69
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Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation. [version 1; peer review: 2 approved, 1 approved with reservations]
Author / Creator:Almeida, Felipe Marques de ; Campos, Tatiana Amabile de ; Pappas Jr, Georgios Joannis
Publisher:England: F1000 Research Ltd
Journal title:F1000 research, 2023, Vol.12, p.1205
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Showing 1 to 20 of 275 results

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Nextflow enables reproducible computational workflows

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TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity

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scalepopgen: Bioinformatic Workflow Resources Implemented in Nextflow for Comprehensive Population Genomic Analyses

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PGSXplorer: an integrated nextflow pipeline for comprehensive quality control and polygenic score model development

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GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data

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RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow

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MultiOmicsIntegrator: a nextflow pipeline for integrated omics analyses

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SpaFlow: a Nextflow pipeline for QC and clustering of MxIF datasets

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BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization

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eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts

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bcRflow: a Nextflow pipeline for characterizing B cell receptor repertoires from non-targeted transcriptomic data

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FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow

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Nextflow vs. plain bash: different approaches to the parallelization of SNP calling from the whole genome sequence data

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nf-rnaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data

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QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data

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Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG [version 1; peer review: awaiting peer review]

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Using the Nextflow framework for reproducible in-silico omics analyses across clusters and clouds

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Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline

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Enhanced protein isoform characterization through long-read proteogenomics

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Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation. [version 1; peer review: 2 approved, 1 approved with reservations]

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