Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Metagenomic next-generation sequencing for the detection of pathogenic microorganisms in community-acquired pneumonia

PROVIDER: PRJNA1131080 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR29746900_1.fastq.gz	Fastqsanger.gz
	SRR29746900_2.fastq.gz	Fastqsanger.gz
	SRR29747000_1.fastq.gz	Fastqsanger.gz
	SRR29747000_2.fastq.gz	Fastqsanger.gz
	SRR29746901_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 336

Similar Datasets

Project description:Pathogenic diagnosis of metagenomic next-generation sequencing compared with culture for patients with community-acquired pneumonia

| PRJNA917446 | ENA

Project description:pathogenic metagenomic next-generation sequencing

| PRJNA1262699 | ENA

Project description:Metagenomic next-generation sequencing of pneumonia patients

| PRJNA729853 | ENA

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

| PRJNA741852 | ENA

Comparative gene and lncRNA expression profiling in patients with severe community acquired pneumonia and healthy controls.

Project description:Investigate the transcriptomic differences between patient with severe community acquired pneumonia (SCAP) and healthy control.

2022-04-18 | GSE196399 | GEO

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-9191 | 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-9189 | biostudies-arrayexpress

Pneumocystis carinii pneumonia Diagnosis via Metagenomic Next-Generation Sequencing

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

| PRJEB43652 | ENA

Chromosomal microarray analysis for validation of the NGS-based CNV detection results in clinical samples

Project description:In order to evaluate the performance of CNV detection in next-generation sequencing platform in varied sample types, we employed chromosomal microarray analysis (CMA) for validation of the samples with NGS-based detection results (NCBI Sequence Read Archive with accession number SRA296708). Besides array Comparative Genomics Hybridization (aCGH, Agilent) , we used a commerical SNP-array (Illumina) including early abortus, induced termination, prenatal samples and postnatal samples. CMA results were compared with NGS-based detection results. 100% consistency was obtained between NGS-based approach and CMA in pathogenic or likely pathogenic CNVs detection.

2015-10-01 | GSE73190 | GEO

Project description:Effect of Metagenomic Next-Generation Sequencing on Clinical Outcomes of Patients with Severe Community-Acquired Pneumonia in the Intensive Care Unit

| PRJNA1000648 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data