ArticleBMC bioinformatics2019
DNAscan: personal computer compatible NGS analysis, annotation and visualisation.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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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
15 citing papers in PubMed.
- An open-source clinical bioinformatics pipeline for real-world NGS implementation: translating genomic variants into actionable treatment strategies in oncology.Journal of translational medicine · 2026Article
- hDNApipe: streamlining human genome analysis and interpretation with an intuitive and user-friendly interface.NAR genomics and bioinformatics · 2025Article
- Investigating the Performance of Oxford Nanopore Long-Read Sequencing with Respect to Illumina Microarrays and Short-Read Sequencing.International journal of molecular sciences · 2025Article
- Modelling Population Genetic Screening in Rare Neurodegenerative Diseases.Biomedicines · 2025Article
- The Role of ctDNA and Liquid Biopsy in the Diagnosis and Monitoring of Head and Neck Cancer: Towards Precision Medicine.Cancers · 2024Review
- COSAP: Comparative Sequencing Analysis Platform.BMC bioinformatics · 2024Article
- Accelerating BWA-MEM Read Mapping on GPUs.ICS ... : proceedings of the ... ACM International Conference on Supercomputing. International Conference on Supercomputing · 2023Article
- DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for human next-generation sequencing data.Bioinformatics (Oxford, England) · 2023Article
- G2P Provides an Integrative Environment for Multi-model genomic selection analysis to improve genotype-to-phenotype prediction.Frontiers in plant science · 2023Article
- VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data.Microbiology spectrum · 2022Article
- The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.F1000Research · 2022Article
- Epilepsy Genetics and Precision Medicine in Adults: A New Landscape for Developmental and Epileptic Encephalopathies.Frontiers in neurology · 2022Review
- An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data.Frontiers in bioinformatics · 2022Article
- DGLinker: flexible knowledge-graph prediction of disease-gene associations.Nucleic acids research · 2021Article
- A Knowledge-Based Machine Learning Approach to Gene Prioritisation in Amyotrophic Lateral Sclerosis.Genes · 2020Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
backgroundNext Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant challenges when dealing with NGS data. Firstly, a huge number of bioinformatics tools for a wide range of uses exist, therefore it is challenging to design an analysis pipeline. Secondly, NGS analysis is computationally intensive, requiring expensive infrastructure, and many medical and research centres do not have adequate high performance computing facilities and cloud computing is not always an option due to privacy and ownership issues. Finally, the interpretation of the results is not trivial and most available pipelines lack the utilities to favour this crucial step.
resultsWe have therefore developed a fast and efficient bioinformatics pipeline that allows for the analysis of DNA sequencing data, while requiring little computational effort and memory usage. DNAscan can analyse a whole exome sequencing sample in 1 h and a 40x whole genome sequencing sample in 13 h, on a midrange computer. The pipeline can look for single nucleotide variants, small indels, structural variants, repeat expansions and viral genetic material (or any other organism). Its results are annotated using a customisable variety of databases and are available for an on-the-fly visualisation with a local deployment of the gene.iobio platform. DNAscan is implemented in Python. Its code and documentation are available on GitHub: https://github.com/KHP-Informatics/DNAscan . Instructions for an easy and fast deployment with Docker and Singularity are also provided on GitHub.
conclusionsDNAscan is an extremely fast and computationally efficient pipeline for analysis, visualization and interpretation of NGS data. It is designed to provide a powerful and easy-to-use tool for applications in biomedical research and diagnostic medicine, at minimal computational cost. Its comprehensive approach will maximise the potential audience of users, bringing such analyses within the reach of non-specialist laboratories, and those from centres with limited funding available.
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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.