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• Education
• Science
• Technology & Computing

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Keywords {🔍}

sequencing, dnascan, article, data, google, scholar, reads, analysis, cas, variants, variant, pipeline, genome, gatk, calling, human, bioinformatics, illumina, dna, viral, speedseq, alignment, research, genetic, results, database, sequence, wgs, panel, annotation, tools, indels, structural, mode, ncbi, sample, repeat, bpw, number, performance, snvs, genomes, calls, london, ngs, intensive, computing, table, res, visualisation,

Topics {✒️}

gov/1000genomes/ftp/technical/working/20101201_cg_na12878/na12878 /khp-informatics/dnascan/blob/master/license high-performance cloud-enabled suite precision=\frac{t_p\ }{t_p+{ sensitivity=\frac{t_p\ }{t_p+{ cpsf6-mediated capsid stabilization arxiv e-prints [internet] chromosome 9p-linked ftd 222-base-long paired reads article download pdf high-throughput sequencing data repeat primed pcr simulation-based comprehensive benchmarking multi-omic data analysis 000-base-pair long deletions haplotype-based variant detection mode recommendations full exon set user-friendly quality control fast gapped-read alignment full access creative commons license snv/indel calling pipeline sequence alignment/map format long repeat expansions privacy choices/manage cookies c9orf72 expansion mutation reported als-related variants /khp-informatics/dnascan burrows-wheeler transform high genotyping quality variant calling precision indel calling precision variant calling assessment adequate internet infrastructure repeat description files open software repository meta variant calling host cell cytoplasm figure 2a shows figure 2b shows variant calling pipelines amyotrophic lateral sclerosis genomic structural variants dna sequencing data genome sequence data stand genomic sci reference human genome human reference genome ncbi id nc_001802

Questions {❓}

• Clinical genetics of amyotrophic lateral sclerosis: what do we really know?

Schema {🗺️}

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         description:Next 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. We 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. DNAscan 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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      name:A. Al-Chalabi
      affiliation:
            name:King’s College London
            address:
               name:Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
               type:PostalAddress
            type:Organization
            name:King’s College Hospital
            address:
               name:King’s College Hospital, London, UK
               type:PostalAddress
            type:Organization
PostalAddress:
      name:Department of Biostatistics and Health Informatics, King’s College London, London, UK
      name:Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
      name:Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
      name:Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
      name:Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
      name:Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
      name:Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK
      name:Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK
      name:Department of Biostatistics and Health Informatics, King’s College London, London, UK
      name:Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK
      name:National Institute for Health Research (NIHR) Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
      name:Department of Biostatistics and Health Informatics, King’s College London, London, UK
      name:Farr Institute of Health Informatics Research, UCL Institute of Health Informatics, University College London, London, UK
      name:National Institute for Health Research (NIHR) Biomedical Research Centre and Dementia Unit at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
      name:Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
      name:King’s College Hospital, London, UK

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