ArticleFrontiers in genetics2016
Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions.
Article in Frontiers in genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
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- Real-World Data and Clinical Implications of Next-Generation Sequencing (NGS)-Based Analysis in Metastatic Breast Cancer Patients.International journal of molecular sciences · 2024Article
- A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset.BMC biology · 2024Article
- c-MYC-dependent transcriptional inhibition of autophagy is implicated in cisplatin sensitivity in HPV-positive head and neck cancer.Cell death & disease · 2023Article
- Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies.International journal of molecular sciences · 2022Review
- New insight into the catalytic -dependent and -independent roles of METTL3 in sustaining aberrant translation in chronic myeloid leukemia.Cell death & disease · 2021Article
- Digital Management Systems in Academic Health Sciences Laboratories: A Scoping Review.Healthcare (Basel, Switzerland) · 2021Article
- Integrated requirement of non-specific and sequence-specific DNA binding in Myc-driven transcription.The EMBO journal · 2021Article
- A scalable high-throughput targeted next-generation sequencing assay for comprehensive genomic profiling of solid tumors.PloS one · 2021Article
- UniqueNAR cancer · 2020Article
- Isabl Platform, a digital biobank for processing multimodal patient data.BMC bioinformatics · 2020Article
- Reactivation of Myc transcription in the mouse heart unlocks its proliferative capacity.Nature communications · 2020Article
- MYC-Associated Factor MAX is a Regulator of the Circadian Clock.International journal of molecular sciences · 2020Article
- A dual role of dLsd1 in oogenesis: regulating developmental genes and repressing transposons.Nucleic acids research · 2020Article
- Macrophages fine tune satellite cell fate in dystrophic skeletal muscle of mdx mice.PLoS genetics · 2019Article
- An early Myc-dependent transcriptional program orchestrates cell growth during B-cell activation.EMBO reports · 2019Article
- Single-cell technologies in reproductive immunology.American journal of reproductive immunology (New York, N.Y. : 1989) · 2019Review
- Article
- Application of next-generation sequencing technology to precision medicine in cancer: joint consensus of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology.Cancer biology & medicine · 2019Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) technologies have deeply changed our understanding of cellular processes by delivering an astonishing amount of data at affordable prices; nowadays, many biology laboratories have already accumulated a large number of sequenced samples. However, managing and analyzing these data poses new challenges, which may easily be underestimated by research groups devoid of IT and quantitative skills. In this perspective, we identify five issues that should be carefully addressed by research groups approaching NGS technologies. In particular, the five key issues to be considered concern: (1) adopting a laboratory management system (LIMS) and safeguard the resulting raw data structure in downstream analyses; (2) monitoring the flow of the data and standardizing input and output directories and file names, even when multiple analysis protocols are used on the same data; (3) ensuring complete traceability of the analysis performed; (4) enabling non-experienced users to run analyses through a graphical user interface (GUI) acting as a front-end for the pipelines; (5) relying on standard metadata to annotate the datasets, and when possible using controlled vocabularies, ideally derived from biomedical ontologies. Finally, we discuss the currently available tools in the light of these issues, and we introduce HTS-flow, a new workflow management system conceived to address the concerns we raised. HTS-flow is able to retrieve information from a LIMS database, manages data analyses through a simple GUI, outputs data in standard locations and allows the complete traceability of datasets, accompanying metadata and analysis scripts.
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