Research graph
References from Software engineering for reproducible pipeline development in bioinformatics. Local targets link to admitted publications; unresolved targets remain external evidence.
Introducing the FAIR principles for research software
10.1038/s41597-022-01710-x · 2022 · External reference
Nextflow enables reproducible computational workflows
10.1038/nbt.3820 · 2017 · External reference
Practical computational reproducibility in the life sciences
10.1016/j.cels.2018.03.014 · 2018 · External reference
ART: a next-generation sequencing read simulator
10.1093/bioinformatics/btr708 · 2012 · External reference
Snakemake—a scalable bioinformatics workflow engine
10.1093/bioinformatics/bts480 · 2012 · External reference
Empowering bioinformatics communities with nextflow and nf-core
10.1186/s13059-025-03673-9 · 2025 · External reference
Auto-phylo: a pipeline maker for phylogenetic studies
2023 · External reference
Compi: a framework for portable and reproducible pipelines
10.7717/peerj-cs.593 · 2021 · External reference
Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites
10.1515/jib-2023-0046 · 2024 · External reference
Unresolved reference
2003 · External reference
FAIRsoft—a practical implementation of FAIR principles for research software
10.1093/bioinformatics/btae464 · 2024 · External reference
Sustainable datas analysis with snakemake
10.12688/f1000research.29032.3 · 2021 · External reference
Sustainable data analysis with snakemake
10.12688/f1000research.29032.3 · 2025 · External reference
Unresolved reference
2026 · External reference
Unresolved reference
2026 · External reference
Workflow systems turn raw data into scientific knowledge
10.1038/d41586-019-02619-z · 2019 · External reference
Seq-gen: an application for the monte carlo simulation of DNA sequence evolution along phylogenetic trees
10.1093/bioinformatics/13.3.235 · 1997 · External reference
Unresolved reference
2026 · External reference
Predicting which mitophagy proteins are dysregulated in spinocerebellar ataxia type 3 (SCA3) using the auto-p2docking pipeline
10.3390/ijms26031325 · 2025 · External reference
