Nextflow | List of Frontiers open access articles

Perspective

Published on 29 Aug 2025

Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers–focused program at The Kids Research Institute Australia

in Integrative Bioinformatics

Patricia Agudelo-Romero
Talya Conradie
Jose Antonio Caparros-Martin
David Jimmy Martino
Anthony Kicic
Stephen Michael Stick
Christopher Hakkaart
Abhinav Sharma
the Theme Collaboration Group

Frontiers in Bioinformatics

doi 10.3389/fbinf.2025.1610015

2,682 views

Technology Report

Published on 28 Jun 2019

Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines

in Computational Genomics

Anthony Federico
Tanya Karagiannis
Kritika Karri
Dileep Kishore
Yusuke Koga
Joshua D. Campbell
Stefano Monti

Frontiers in Genetics

doi 10.3389/fgene.2019.00614

14,680 views
19 citations

Methods

Published on 27 Sep 2022

scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data

in Developmental Epigenetics

Kai Hu
Haibo Liu
Nathan D. Lawson
Lihua Julie Zhu

Frontiers in Cell and Developmental Biology

doi 10.3389/fcell.2022.981859

18,417 views
9 citations

Technology and Code

Published on 28 Oct 2022

MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data

in Evolutionary and Genomic Microbiology

Daria Shafranskaya
Varsha Kale
Rob Finn
Alla L. Lapidus
Anton Korobeynikov
Andrey D. Prjibelski

Frontiers in Microbiology

doi 10.3389/fmicb.2022.981458

10,034 views
10 citations

Methods

Published on 24 Sep 2020

GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline

in Computational Genomics

José Afonso Guerra-Assunção
Lucia Conde
Ismail Moghul
Amy P. Webster
Simone Ecker
Olga Chervova
Christina Chatzipantsiou
Pablo P. Prieto
Stephan Beck
Javier Herrero

Frontiers in Genetics

doi 10.3389/fgene.2020.518644

6,991 views
5 citations

Technology and Code

Published on 17 Mar 2020

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets

in Computational Genomics

Luca Cozzuto
Huanle Liu
Leszek P. Pryszcz
Toni Hermoso Pulido
Anna Delgado-Tejedor
Julia Ponomarenko
Eva Maria Novoa

Frontiers in Genetics

doi 10.3389/fgene.2020.00211

53,734 views
60 citations

Technology and Code

Published on 01 Mar 2022

CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification

in Genomic Analysis

Marieke Vromman
Jasper Anckaert
Jo Vandesompele
Pieter-Jan Volders

Frontiers in Bioinformatics

doi 10.3389/fbinf.2022.834655

7,904 views
9 citations

Original Research

Published on 26 Nov 2020

Accurate and Efficient KIR Gene and Haplotype Inference From Genome Sequencing Reads With Novel K-mer Signatures

in Alloimmunity and Transplantation

David Roe
Rui Kuang

Frontiers in Immunology

doi 10.3389/fimmu.2020.583013

6,432 views
20 citations

Articles

Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers–focused program at The Kids Research Institute Australia

Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines

scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data

MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data

GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets

CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification

Accurate and Efficient KIR Gene and Haplotype Inference From Genome Sequencing Reads With Novel K-mer Signatures