Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers

Streamlining data-intensive biology with workflow systems

(2021) Taylor Reiter et al.   GigaScience

Reproducibility in systems biology modelling

(2021) Krishna Tiwari et al.   Molecular Systems Biology

Using prototyping to choose a bioinformatics workflow management system

(2021) Michael Jackson et al.   PLoS Computational Biology

Butler enables rapid cloud-based analysis of thousands of human genomes

(2020) Sergei Yakneen et al.   NATURE BIOTECHNOLOGY

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

Bench pressing with genomics benchmarkers

(2020) Vivien Marx   NATURE METHODS

Tximeta: Reference sequence checksums for provenance identification in RNA-seq

(2020) Michael I. Love et al.   PLoS Computational Biology

Toward a domain‐specific language for scientific workflow‐based applications on multicloud system

(2020) Gennaro Cordasco et al.   CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE

Variability in the analysis of a single neuroimaging dataset by many teams

(2020) Rotem Botvinik-Nezer et al.   NATURE

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

(2020) Vahid Jalili et al.   NUCLEIC ACIDS RESEARCH

Better together: Elements of successful scientific software development in a distributed collaborative community

(2020) Julia Koehler Leman et al.   PLoS Computational Biology

Seven quick tips for analysis scripts in neuroimaging

(2020) Marijn van Vliet   PLoS Computational Biology

PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection

(2020) Martin Hölzer et al.   BIOINFORMATICS

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

(2020) Silas Kieser et al.   BMC BIOINFORMATICS

Scalability and cost-effectiveness analysis of whole genome-wide association studies on Google Cloud Platform and Amazon Web Services

(2020) Inès Krissaane et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Ten recommendations for supporting open pathogen genomic analysis in public health

(2020) Allison Black et al.   NATURE MEDICINE

Data Lakes, Clouds, and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data

(2019) Robert L. Grossman   TRENDS IN GENETICS

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis

(2019) Vivek Bhardwaj et al.   BIOINFORMATICS

In silico analysis of RNA-seq requires a more complete description of methodology

(2019) Joël Simoneau et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines

(2019) Samuel Lampa et al.   GigaScience

How to support open-source software and stay sane

(2019) Anna Nowogrodzki   NATURE

Challenges and recommendations to improve the installability and archival stability of omics computational tools

(2019) Serghei Mangul et al.   PLOS BIOLOGY

CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language

(2019) Michael Kotliar et al.   GigaScience

GenPipes: an open-source framework for distributed and scalable genomic analyses

(2019) Mathieu Bourgey et al.   GigaScience

Why reinventing the wheels? An empirical study on library reuse and re-implementation

(2019) Bowen Xu et al.   EMPIRICAL SOFTWARE ENGINEERING

Workflow systems turn raw data into scientific knowledge

(2019) Jeffrey M. Perkel   NATURE

Current RNA-seq methodology reporting limits reproducibility

(2019) Joël Simoneau et al.   BRIEFINGS IN BIOINFORMATICS

Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines

(2019) Yasset Perez‐Riverol et al.   PROTEOMICS

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

(2018) MacIntosh Cornwell et al.   BMC BIOINFORMATICS

An empirical comparison of dependency network evolution in seven software packaging ecosystems

(2018) Alexandre Decan et al.   EMPIRICAL SOFTWARE ENGINEERING

LncPipe: A Nextflow-based pipeline for identification and analysis of long non-coding RNAs from RNA-Seq data

(2018) Qi Zhao et al.   Journal of Genetics and Genomics

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Cloud computing for genomic data analysis and collaboration

(2018) Ben Langmead et al.   NATURE REVIEWS GENETICS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

An empirical analysis of journal policy effectiveness for computational reproducibility

(2018) Victoria Stodden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Practical Computational Reproducibility in the Life Sciences

(2018) Björn Grüning et al.   Cell Systems

Community-Driven Data Analysis Training for Biology

(2018) Bérénice Batut et al.   Cell Systems

Container-based bioinformatics with Pachyderm

(2018) Jon Ander Novella et al.   BIOINFORMATICS

Raw data queries during data-intensive parallel workflow execution

(2017) Vítor Silva et al.   Future Generation Computer Systems-The International Journal of eScience

KNIME for reproducible cross-domain analysis of life science data

(2017) Alexander Fillbrunn et al.   JOURNAL OF BIOTECHNOLOGY

Software simplified

(2017) Andrew Silver   NATURE

Reproducibility of computational workflows is automated using continuous analysis

(2017) Brett K Beaulieu-Jones et al.   NATURE BIOTECHNOLOGY

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Toil enables reproducible, open source, big biomedical data analyses

(2017) John Vivian et al.   NATURE BIOTECHNOLOGY

Ten Simple Rules for Developing Usable Software in Computational Biology

(2017) Markus List et al.   PLoS Computational Biology

Scalability and Validation of Big Data Bioinformatics Software

(2017) Andrian Yang et al.   Computational and Structural Biotechnology Journal

Singularity: Scientific containers for mobility of compute

(2017) Gregory M. Kurtzer et al.   PLoS One

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Bpipe: a tool for running and managing bioinformatics pipelines

(2012) Simon P. Sadedin et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

A modular package manager architecture

(2012) Pietro Abate et al.   INFORMATION AND SOFTWARE TECHNOLOGY

The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements

(2012) Ed H. B. M. Gronenschild et al.   PLoS One

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY