ArticleGigaScience2019
GenPipes: an open-source framework for distributed and scalable genomic analyses.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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Who cites it
115 citing papers in PubMed.
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- PTPN11-Related Noonan Syndrome Predisposes to Multifocal Low-Grade CNS Tumors Harboring FGFR1 Variants.Research square · 2026Article
- Metagenome-assembled genomes from the temperate forest phyllosphere in Eastern Canada.Access microbiology · 2026Article
- Coordinated plant and microbial transcriptional responses to oil-sands process-affected water.ISME communications · 2026Article
- Benchmarking of Oxford Nanopore whole genome sequencing for germline variant and CpG methylation detection across Canada's national platform for genome sequencing and analysis.Frontiers in genetics · 2026Article
- TARDBP (TDP-43) Knock-in Zebrafish Display a Late-Onset Motor Phenotype and Loss of Large Spinal Cord Motor Neurons.Annals of neurology · 2026Article
- A novel H2A-A127 variant is associated with human cancer and enhances tumor-related phenotypes inFrontiers in oncology · 2026Article
- Analysis Methods for Diagnosing Rare Neurodevelopmental Diseases with Episignatures: A Systematic Review of the Literature.Biomedicines · 2025Review
- Gastrectomy promoted diabetes remission involves the molecular clock and epigenetic mechanisms in a rat model of lean type 2 diabetes.Scientific reports · 2025Article
- RnaXtract, a tool for extracting gene expression, variants, and cell-type composition from bulk RNA sequencing.Scientific reports · 2025Article
- REST/NRSF Preserves muscle stem cell identity by repressing alternate cell fate.Nature communications · 2025Article
- Sustained YAP1 signaling alters the fates of lutein and Müllerian mesenchymal cells in mice.Reproduction (Cambridge, England) · 2025Article
55 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
23 authors.
Funding
Abstract
backgroundWith the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing is growing.
findingsHere we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for high-performance computing clusters and the cloud. GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA sequencing, chromatin immunoprecipitation sequencing, DNA sequencing, methylation sequencing, Hi-C, capture Hi-C, metagenomics, and Pacific Biosciences long-read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has already been configured on several servers, and a Docker image is also available to facilitate additional installations.
conclusionsGenPipes offers genomics researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.