Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Diagnosis of infective endocarditis by using metagenomic next-generation sequencing

PROVIDER: PRJNA784716 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17071500.fastq.gz	Fastqsanger.gz
	SRR17071501.fastq.gz	Fastqsanger.gz
	SRR17071601.fastq.gz	Fastqsanger.gz
	SRR17071502.fastq.gz	Fastqsanger.gz
	SRR17071503.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 154

Similar Datasets

Project description:Diagnosis of infective endocarditis by using metagenomic next-generation sequencing

| PRJNA784716 | ENA

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): from reads to pathogens. A specific and exhaustive pipeline for handling metagenomic shotgun sequencing data.

Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.

2021-07-26 | E-MTAB-9189 | biostudies-arrayexpress

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): from reads to pathogens. A specific and exhaustive pipeline for handling metagenomic shotgun sequencing data.

2021-07-26 | E-MTAB-9191 | biostudies-arrayexpress

Identification of host endotypes using peripheral blood transcriptomics in a prospective cohort of patients with endocarditis [pre-post_qx]

Project description:Infective endocarditis is a severe disease caused by the infection of heart valves and endocardium by pathogenic germ. Antimicrobial therapy and surgery remain the basis of treatment, and up to 50% of the patients require surgical replacement of the affected valves to control the infectious source. The objective of this work is to identify the existence of endotypes in a prospective cohort of patients with infective endocarditis. We performed a bulk RNA-seq form peripheral blood to cluster patients according to their transcriptomic profiles at diagnosis and during their follow-up. Clinical data, outcomes and response to surgery were assessed in a cluster-specific manner, in order to identify differences in the pathogenesis that could help to find personalized treatments and improve the outcome.

2023-08-08 | GSE240320 | GEO

Identification of host endotypes using peripheral blood transcriptomics in a prospective cohort of patients with endocarditis [pre]

2023-08-08 | GSE240319 | GEO

human metagenome

Project description:Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis

| PRJNA298217 | ENA

Project description:Pneumonia diagnosis based on metagenomic next-generation sequencing

| PRJNA741852 | ENA

Pneumocystis carinii pneumonia Diagnosis via Metagenomic Next-Generation Sequencing

Project description:Pneumocystis carinii pneumonia Diagnosis via Metagenomic Next-Generation Sequencing

| PRJEB43652 | ENA

Project description:metagenomic next-generation sequencing for the diagnosis of OIAI