Vulture: cloud-enabled scalable mining of microbial reads in public scRNA-seq data.
Gigascience
; 132024 01 02.
Article
em En
| MEDLINE
| ID: mdl-38195165
ABSTRACT
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.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Temas:
Geral
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Tipos_de_cancer
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Outros_tipos
Base de dados:
MEDLINE
Assunto principal:
Carcinoma Hepatocelular
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Neoplasias Hepáticas
Limite:
Humans
Idioma:
En
Revista:
Gigascience
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
China