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A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection

ABSTRACT: A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection

PROVIDER: PRJEB27711 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2819900.fastq.gz	Fastqsanger.gz
	ERR2819910.fastq.gz	Fastqsanger.gz
	ERR2819901.fastq.gz	Fastqsanger.gz
	ERR2819911.fastq.gz	Fastqsanger.gz
	ERR2819902.fastq.gz	Fastqsanger.gz

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A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection.

Project description:Metagenomics is currently the only generic method for pathogen detection. Starting from RNA allows the assessment of the whole sample community including RNA viruses. Here we present our modular concerted protocol for sample processing for diagnostic metagenomics analysis of human, animal, and food samples. The workflow does not rely on dedicated amplification steps at any stage in the process and, in contrast to published methods, libraries prepared accordingly will yield only minute amounts of unclassifiable reads. We confirmed the performance of the approach using a spectrum of pathogen/matrix-combinations showing it has the potential to become a commonly usable analytical framework.

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A Versatile Processing Workflow to Enable Pathogen Detection in Clinical Samples from Organs Using VIDISCA.

Project description:In recent years, refined molecular methods coupled with powerful high throughput sequencing technologies have increased the potential of virus discovery in clinical samples. However, host genetic material remains a complicating factor that interferes with discovery of novel viruses in solid tissue samples as the relative abundance of the virus material is low. Physical enrichment processing methods, although usually complicated, labor-intensive, and costly, have proven to be successful for improving sensitivity of virus detection in complex samples. In order to further increase detectability, we studied the application of fast and simple high-throughput virus enrichment methods on tissue homogenates. Probe sonication in high EDTA concentrations, organic extraction with Vertrel™ XF, or a combination of both, were applied prior to chromatography-like enrichment using Capto™ Core 700 resin, after which effects on virus detection sensitivity by the VIDISCA method were determined. Sonication in the presence of high concentrations of EDTA showed the best performance with an increased proportion of viral reads, up to 9.4 times, yet minimal effect on the host background signal. When this sonication procedure in high EDTA concentrations was followed by organic extraction with Vertrel™ XF and two rounds of core bead chromatography enrichment, an increase up to 10.5 times in the proportion of viral reads in the processed samples was achieved, with reduction of host background sequencing. We present a simple and semi-high-throughput method that can be used to enrich homogenized tissue samples for viral reads.

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Pectobacterium versatile

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Mapping SET1B Chromatin Interactions with DamID using DamMapper, a Comprehensive Snakemake Workflow

Project description:Background DNA adenine methyltransferase identification followed by sequencing (DamID-seq) is a powerful method used to map genome-wide chromatin-protein interactions. However, the bioinformatic analysis of DamID-seq data presents significant challenges due to the inherent complexities of the data and a notable lack of comprehensive software solutions for data-processing and downstream analysis. Results To address these challenges, we present a comprehensive bioinformatic workflow for DamID-seq data analysis, DamMapper, using the Snakemake workflow management system. Key features include straightforward processing of multiple biological replicates, visualisation of quality control figures, such as a correlation heatmaps and principal component analysis (PCA) plotting, and robust code quality maintained through continuous integration (CI). Reproducibility is ensured across diverse computational environments, including cloud computing and high-performance computing (HPC) clusters, through the implementation of software environments (Conda) and containerisation (Docker/Apptainer). We validated this workflow using a previously published DamID-seq dataset and Furthermore, we apply it to analyse novel datasets for proteins involved in the hypoxia response, specifically the transcription factor HIF-1α and the histone methyltransferase SET1B. This application reveals a strong concordance between our HIF-1α DamID-seq results and ChIP-seq data, and importantly, provides the first genome-wide DNA binding map for SET1B. Conclusions This work provides a validated, reproducible, and feature-rich workflow that overcomes common hurdles in DamID-seq data analysis. By streamlining the processing and ensuring robustness, DamMapper facilitates reliable analysis and enables new biological discoveries, as demonstrated by the characterization of SET1B binding sites. The workflow is available under the MIT license at: https://github.com/niekwit/damid-seq.

2025-08-21 | GSE296995 | GEO

A Bioconductor workflow for processing, evaluating and interpreting expression proteomics data: Case data

Project description:Files associated with "A Bioconductor workflow for processing, evaluating and interpreting expression proteomics data".

2023-06-29 | PXD041794 | Pride

Pectobacterium versatile strain:21A26

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Pectobacterium versatile strain:GP16

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2024-12-19 | GSE284395 | GEO

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