ArticleGigaScience2020
Refgenie: a reference genome resource manager.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
34 citing papers in PubMed, 58 citations in OpenAlex.
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- Polyamine Depletion by D,L-α-Difluoromethylornithine Inhibits Ewing Sarcoma Metastasis by Inducing Ferroptosis.Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Article
- High-coverage allele-resolved single-cell DNA methylation profiling reveals cell lineage, X-inactivation state, and replication dynamics.Nature communications · 2025Article
- PRMT5 activity sustains histone production to maintain genome integrity.bioRxiv : the preprint server for biology · 2025Article
- CHOIR improves significance-based detection of cell types and states from single-cell data.Nature genetics · 2025Article
- Cancer associated fibroblasts drive epithelial to mesenchymal transition and classical to basal change in pancreatic ductal adenocarcinoma cells with loss of IL-8 expression.bioRxiv : the preprint server for biology · 2025Article
- SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline.Briefings in bioinformatics · 2024Article
- Compromised transcription-mRNA export factor THOC2 causes R-loop accumulation, DNA damage and adverse neurodevelopment.Nature communications · 2024Article
- ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management.BMC bioinformatics · 2024Article
- SciDataFlow: a tool for improving the flow of data through science.Bioinformatics (Oxford, England) · 2024Article
- An approach for prioritizing candidate genes from RNA-seq using preclinical cocaine self-administration datasets as a test case.G3 (Bethesda, Md.) · 2023Article
- Globally elevated levels of histone H3 lysine 9 trimethylation in early infancy are associated with poor growth trajectory in Bangladeshi children.Clinical epigenetics · 2023Article
- genomepy: genes and genomes at your fingertips.Bioinformatics (Oxford, England) · 2023Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundReference genome assemblies are essential for high-throughput sequencing analysis projects. Typically, genome assemblies are stored on disk alongside related resources; e.g., many sequence aligners require the assembly to be indexed. The resulting indexes are broadly applicable for downstream analysis, so it makes sense to share them. However, there is no simple tool to do this.
resultsHere, we introduce refgenie, a reference genome assembly asset manager. Refgenie makes it easier to organize, retrieve, and share genome analysis resources. In addition to genome indexes, refgenie can manage any files related to reference genomes, including sequences and annotation files. Refgenie includes a command line interface and a server application that provides a RESTful API, so it is useful for both tool development and analysis.
conclusionsRefgenie streamlines sharing genome analysis resources among groups and across computing environments. Refgenie is available at https://refgenie.databio.org.
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Registered trials
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.