دورية أكاديمية
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Vulture: cloud-enabled scalable mining of microbial reads in public scRNA-seq data.

التفاصيل البيبلوغرافية
العنوان: Vulture: cloud-enabled scalable mining of microbial reads in public scRNA-seq data.
المؤلفون: Chen J; Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China.; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China., Yin D; Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China.; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China., Wong HYH; Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China., Duan X; Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China., Yu KHO; Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China.; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China., Ho JWK; Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China.; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
المصدر: GigaScience [Gigascience] 2024 Jan 02; Vol. 13.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: United States NLM ID: 101596872 Publication Model: Print Cited Medium: Internet ISSN: 2047-217X (Electronic) Linking ISSN: 2047217X NLM ISO Abbreviation: Gigascience Subsets: MEDLINE
أسماء مطبوعة: Publication: 2017- : New York : Oxford University Press
Original Publication: London : BioMed Central
مواضيع طبية MeSH: Carcinoma, Hepatocellular*/genetics , Liver Neoplasms*, Humans ; Benchmarking ; DNA Copy Number Variations ; Hepatitis B virus ; Single-Cell Gene Expression Analysis
مستخلص: The rapidly growing collection of public single-cell sequencing data has become a valuable resource for molecular, cellular, and microbial discovery. Previous studies mostly overlooked detecting pathogens in human single-cell sequencing data. Moreover, existing bioinformatics tools lack the scalability to deal with big public data. We introduce Vulture, a scalable cloud-based pipeline that performs microbial calling for single-cell RNA sequencing (scRNA-seq) data, enabling meta-analysis of host-microbial studies from the public domain. In our benchmarking experiments, Vulture is 66% to 88% faster than local tools (PathogenTrack and Venus) and 41% faster than the state-of-the-art cloud-based tool Cumulus, while achieving comparable microbial read identification. In terms of the cost on cloud computing systems, Vulture also shows a cost reduction of 83% ($12 vs. ${\$}$70). We applied Vulture to 2 coronavirus disease 2019, 3 hepatocellular carcinoma (HCC), and 2 gastric cancer human patient cohorts with public sequencing reads data from scRNA-seq experiments and discovered cell type-specific enrichment of severe acute respiratory syndrome coronavirus 2, hepatitis B virus (HBV), and Helicobacter pylori-positive cells, respectively. In the HCC analysis, all cohorts showed hepatocyte-only enrichment of HBV, with cell subtype-associated HBV enrichment based on inferred copy number variations. In summary, Vulture presents a scalable and economical framework to mine unknown host-microbial interactions from large-scale public scRNA-seq data. Vulture is available via an open-source license at https://github.com/holab-hku/Vulture.
(© The Author(s) 2024. Published by Oxford University Press GigaScience.)
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معلومات مُعتمدة: Innovation and Technology Commission - Hong Kong
فهرسة مساهمة: Keywords: COVID-19; HCC; cloud computing; single cell; virus
تواريخ الأحداث: Date Created: 20240109 Date Completed: 20240124 Latest Revision: 20240724
رمز التحديث: 20240726
مُعرف محوري في PubMed: PMC10776309
DOI: 10.1093/gigascience/giad117
PMID: 38195165
قاعدة البيانات: MEDLINE
الوصف
تدمد:2047-217X
DOI:10.1093/gigascience/giad117