{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,30]],"date-time":"2025-08-30T16:54:46Z","timestamp":1756572886372,"version":"3.40.5"},"posted":{"date-parts":[[2025,3,19]]},"reference-count":0,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T00:00:00Z","timestamp":1742342400000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<p>Metagenomic bioinformatics pipelines are essential for extracting meaningful biological insights from the vast amounts of sequencing data generated in microbial studies. However, current approaches face several challenges that limit their utility and accessibility.  A major hurdle is the efficient and accurate removal of human DNA reads from metagenomic datasets, a critical step for improving the sensitivity of pathogen detection. This process often demands significant computational resources and can become a bottleneck in large-scale analyses. In addition, most existing pipelines are designed to focus on specific microbial groups, making it difficult to comprehensively analyse the full spectrum of microbial communities, including bacteria and viruses, from a single sample. This lack of unified, end-to-end solutions limits both the scope and reproducibility of metagenomic research.  To address these limitations, we developed a comprehensive protocol that streamlines host DNA removal and enables the simultaneous profiling of diverse microbial taxa from a single FASTQ file. This workflow consolidates existing pipelines within a unified framework, optimising computational efficiency while producing comprehensive microbial profiles. Our approach bridges a critical gap in metagenomics by supporting both clinical and environmental research needs in a scalable and conscious manner. <\/p>","DOI":"10.17504\/protocols.io.36wgq6rdolk5\/v2","type":"posted-content","created":{"date-parts":[[2025,5,12]],"date-time":"2025-05-12T10:25:25Z","timestamp":1747045525000},"source":"Crossref","is-referenced-by-count":1,"title":["Metagenome Processing in Clinical Setting for Respiratory Pathogens v2"],"prefix":"10.17504","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6402-6993","authenticated-orcid":false,"given":"Abhinav","family":"Sharma","sequence":"first","affiliation":[]},{"given":"Jose","family":"A Caparros-Martin","sequence":"additional","affiliation":[]},{"given":"Patricia","family":"Agudelo-Romero","sequence":"additional","affiliation":[]}],"member":"297","container-title":[],"original-title":[],"deposited":{"date-parts":[[2025,5,12]],"date-time":"2025-05-12T10:25:25Z","timestamp":1747045525000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.protocols.io\/view\/metagenome-processing-in-clinical-setting-for-resp-gy78bxzrx"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,19]]},"references-count":0,"URL":"https:\/\/doi.org\/10.17504\/protocols.io.36wgq6rdolk5\/v2","relation":{"is-version-of":[{"id-type":"doi","id":"10.17504\/protocols.io.36wgq6rdolk5\/v1","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2025,3,19]]},"subtype":"preprint"}}