ArticleJournal of pathology informatics2016
Use of application containers and workflows for genomic data analysis.
Article in Journal of pathology informatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- Article
- A complete pedigree-based graph workflow for rare candidate variant analysis.Genome research · 2022Article
- Federated analysis of BRCA1 and BRCA2 variation in a Japanese cohort.Cell genomics · 2022Article
- nf-rnaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data.South African computer journal = Suid-Afrikaanse rekenaartydskrif · 2021Article
- Design considerations for workflow management systems use in production genomics research and the clinic.Scientific reports · 2021Article
- Bridging the Collaboration Gap: Real-time Identification of Clinical Specimens for Biomedical Research.Journal of pathology informatics · 2020Article
- Container-based bioinformatics with Pachyderm.Bioinformatics (Oxford, England) · 2019Article
- OMeta: an ontology-based, data-driven metadata tracking system.BMC bioinformatics · 2019Article
- Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics.BMC bioinformatics · 2018Article
- Hot-starting software containers for STAR aligner.GigaScience · 2018Article
- Reproducible Bioconductor workflows using browser-based interactive notebooks and containers.Journal of the American Medical Informatics Association : JAMIA · 2018Article
- Article
- META-pipe cloud setup and execution.F1000Research · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundThe rapid acquisition of biological data and development of computationally intensive analyses has led to a need for novel approaches to software deployment. In particular, the complexity of common analytic tools for genomics makes them difficult to deploy and decreases the reproducibility of computational experiments.
methodsRecent technologies that allow for application virtualization, such as Docker, allow developers and bioinformaticians to isolate these applications and deploy secure, scalable platforms that have the potential to dramatically increase the efficiency of big data processing.
resultsWhile limitations exist, this study demonstrates a successful implementation of a pipeline with several discrete software applications for the analysis of next-generation sequencing (NGS) data.
conclusionsWith this approach, we significantly reduced the amount of time needed to perform clonal analysis from NGS data in acute myeloid leukemia.
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What OpenQuestion holds
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.