Design and implementation of a metagenomic analytical pipeline for respiratory pathogen detection.

ABSTRACT:

Objective

We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment.

Results

We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4 min per sample (processing 1 million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a corr

SUBMITTER: Viana PAB 

PROVIDER: S-EPMC11451226 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature