Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Search Page

Filters

My NCBI Filters

Results by year

Table representation of search results timeline featuring number of search results per year.

Year Number of Results
2017 1
2019 1
2020 2
2021 5
2022 1
2023 4

Text availability

Article attribute

Article type

Publication date

Search Results

14 results

Results by year

Citations

1 article found by citation matching

Search results

Filters applied: . Clear all
Page 1
Nextflow enables reproducible computational workflows.
Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Di Tommaso P, et al. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. Nat Biotechnol. 2017. PMID: 28398311 No abstract available.
scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data.
Hu K, Liu H, Lawson ND, Zhu LJ. Hu K, et al. Front Cell Dev Biol. 2022 Sep 27;10:981859. doi: 10.3389/fcell.2022.981859. eCollection 2022. Front Cell Dev Biol. 2022. PMID: 36238687 Free PMC article.
Although numerous software tools and pipelines have been developed, an easy-to-use, scalable, reproducible, and comprehensive pipeline for scATAC-seq data analyses is still lacking. To fill this gap, we developed scATACpipe, a Nextflow pipeline, for performing compr …
Although numerous software tools and pipelines have been developed, an easy-to-use, scalable, reproducible, and comprehensive pipelin …
Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines.
Federico A, Karagiannis T, Karri K, Kishore D, Koga Y, Campbell JD, Monti S. Federico A, et al. Front Genet. 2019 Jun 28;10:614. doi: 10.3389/fgene.2019.00614. eCollection 2019. Front Genet. 2019. PMID: 31316552 Free PMC article.
The Pipeliner framework provides an out-of-the-box solution for processing various types of sequencing data. It combines the Nextflow scripting language and Anaconda package manager to generate modular computational workflows. ...This report highlights the de …
The Pipeliner framework provides an out-of-the-box solution for processing various types of sequencing data. It combines the Nextflow …
nf-rnaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data.
Mpangase PT, Frost J, Tikly M, Ramsay M, Hazelhurst S. Mpangase PT, et al. S Afr Comput J. 2021 Dec;33(2):830. doi: 10.18489/sacj.v33i2.830. Epub 2021 Dec 20. S Afr Comput J. 2021. PMID: 35574063 Free PMC article.
Using Nextflow as a workflow management system and Singularity for application containerisation, the nf-rnaSeqCount pipeline was developed for mapping raw RNA-seq reads to a reference genome and quantifying abundance of identified genomic features for differential g …
Using Nextflow as a workflow management system and Singularity for application containerisation, the nf-rnaSeqCount pipeline w …
nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis.
West C, Capitanchik C, Cheshire C, Luscombe NM, Chakrabarti A, Ule J. West C, et al. Wellcome Open Res. 2023 Jul 4;8:286. doi: 10.12688/wellcomeopenres.19453.1. eCollection 2023. Wellcome Open Res. 2023. PMID: 37829674 Free PMC article.
There has been a proliferation of CLIP-based experimental protocols, as well as computational tools, especially for peak-calling. Consequently, there is an urgent need for a well-documented bioinformatic pipeline that enshrines the principles of robustness, reproducibil …
There has been a proliferation of CLIP-based experimental protocols, as well as computational tools, especially for peak-calling. Con …
RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow.
Lataretu M, Hölzer M. Lataretu M, et al. Genes (Basel). 2020 Dec 10;11(12):1487. doi: 10.3390/genes11121487. Genes (Basel). 2020. PMID: 33322033 Free PMC article.
Although RNA-Seq evolved into a standard technique, there is no universal gold standard for these data's computational analysis. On top of that, previous studies proved the irreproducibility of RNA-Seq studies. Here, we present a portable, scalable, and parallelizab …
Although RNA-Seq evolved into a standard technique, there is no universal gold standard for these data's computational analysi …
eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity.
Mousavi-Derazmahalleh M, Stott A, Lines R, Peverley G, Nester G, Simpson T, Zawierta M, De La Pierre M, Bunce M, Christophersen CT. Mousavi-Derazmahalleh M, et al. Mol Ecol Resour. 2021 Jul;21(5):1697-1704. doi: 10.1111/1755-0998.13356. Epub 2021 Mar 9. Mol Ecol Resour. 2021. PMID: 33580619
This pipeline is based on Nextflow and Singularity which enable a scalable, portable and reproducible workflow using software containers on a local computer, clouds and high-performance computing (HPC) clusters. ...To our knowledge, this …
This pipeline is based on Nextflow and Singularity which enable a scalable, portable and reproducible workflow u …
The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols.
Yuen D, Cabansay L, Duncan A, Luu G, Hogue G, Overbeck C, Perez N, Shands W, Steinberg D, Reid C, Olunwa N, Hansen R, Sheets E, O'Farrell A, Cullion K, O'Connor BD, Paten B, Stein L. Yuen D, et al. Nucleic Acids Res. 2021 Jul 2;49(W1):W624-W632. doi: 10.1093/nar/gkab346. Nucleic Acids Res. 2021. PMID: 33978761 Free PMC article.
Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows. The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Acces …
Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows …
Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality.
Albanese D, Donati C. Albanese D, et al. F1000Res. 2021 Aug 17;10:822. doi: 10.12688/f1000research.54418.1. eCollection 2021. F1000Res. 2021. PMID: 35136576 Free PMC article.
Assessing the quality of genomes recovered from metagenomes requires the use of complex pipelines involving many independent steps, often difficult to reproduce and maintain. A comprehensive, automated and easy-to-use computational workflow for the quality assessmen …
Assessing the quality of genomes recovered from metagenomes requires the use of complex pipelines involving many independent steps, often di …
DolphinNext: a distributed data processing platform for high throughput genomics.
Yukselen O, Turkyilmaz O, Ozturk AR, Garber M, Kucukural A. Yukselen O, et al. BMC Genomics. 2020 Apr 19;21(1):310. doi: 10.1186/s12864-020-6714-x. BMC Genomics. 2020. PMID: 32306927 Free PMC article.
We complement these new platforms by providing a graphical user interface to create, maintain, and execute complex pipelines. Such a platform will simplify robust and reproducible workflow creation for non-technical users as well as provide a robust platform to main …
We complement these new platforms by providing a graphical user interface to create, maintain, and execute complex pipelines. Such a platfor …
14 results