ArticleBioinformatics (Oxford, England)2014
NGSANE: a lightweight production informatics framework for high-throughput data analysis.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer.Nature communications · 2020Article
- Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains.Nature communications · 2020Article
- Article
- System for Quality-Assured Data Analysis: Flexible, reproducible scientific workflows.Genetic epidemiology · 2019Article
- Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups.Epigenetics & chromatin · 2019Article
- iRODS metadata management for a cancer genome analysis workflow.BMC bioinformatics · 2019Article
- Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum "Latescibacteria" (WS3).Applied and environmental microbiology · 2017Article
- SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis.BMC bioinformatics · 2016Article
- Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations.Genome research · 2016Article
- Targeted next-generation sequencing of 22 mismatch repair genes identifies Lynch syndrome families.Cancer medicine · 2016Article
- Genome-wide analysis of chemically induced mutations in mouse in phenotype-driven screens.BMC genomics · 2015Article
- Long Non-Coding RNA Expression during Aging in the Human Subependymal Zone.Frontiers in neurology · 2015Article
- Cpipe: a shared variant detection pipeline designed for diagnostic settings.Genome medicine · 2015Article
- 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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryThe initial steps in the analysis of next-generation sequencing data can be automated by way of software 'pipelines'. However, individual components depreciate rapidly because of the evolving technology and analysis methods, often rendering entire versions of production informatics pipelines obsolete. Constructing pipelines from Linux bash commands enables the use of hot swappable modular components as opposed to the more rigid program call wrapping by higher level languages, as implemented in comparable published pipelining systems. Here we present Next Generation Sequencing ANalysis for Enterprises (NGSANE), a Linux-based, high-performance-computing-enabled framework that minimizes overhead for set up and processing of new projects, yet maintains full flexibility of custom scripting when processing raw sequence data. AVAILABILITY AND IMPLEMENTATION: Ngsane is implemented in bash and publicly available under BSD (3-Clause) licence via GitHub at https://github.com/BauerLab/ngsane. CONTACT: Denis.Bauer@csiro.au SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.