SoEM-Web: a user-friendly platform for the analysis and visualization of small-organelle-enriched metagenomics data
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| Pubblicato in: | bioRxiv (Feb 16, 2025) |
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| Autore principale: | |
| Altri autori: | , |
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Cold Spring Harbor Laboratory Press
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| Accesso online: | Citation/Abstract Full text outside of ProQuest |
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| 001 | 3167424025 | ||
| 003 | UK-CbPIL | ||
| 022 | |a 2692-8205 | ||
| 024 | 7 | |a 10.1101/2025.02.12.637736 |2 doi | |
| 035 | |a 3167424025 | ||
| 045 | 0 | |b d20250216 | |
| 100 | 1 | |a Oh, Jooseong | |
| 245 | 1 | |a SoEM-Web: a user-friendly platform for the analysis and visualization of small-organelle-enriched metagenomics data | |
| 260 | |b Cold Spring Harbor Laboratory Press |c Feb 16, 2025 | ||
| 513 | |a Working Paper | ||
| 520 | 3 | |a Background: Marine microeukaryotes play a crucial role in global biogeochemical cycles and ecosystem functioning. However, their diversity and distribution patterns remain poorly understood. To improve the biodiversity assessment of environmental samples, we recently developed a PCR-free, small-organelle-enriched metagenomics (SoEM) method, accompanied by a bioinformatics workflow for analyzing SoEM metagenomic data. However, the complexity of these analyses typically requires extensive bioinformatics expertise, potentially limiting their broader adoption. Methods: To address this challenge, we present SoEM-Web, a user-friendly web application for the interactive analysis, classification, and visualization of SoEM metagenomic data. SoEM-Web integrates all necessary procedures, including raw sequencing data preprocessing, paired-end read merging, automated taxonomic identification, and diversity visualization, into a streamlined workflow accessible through an intuitive interface. This application is designed to facilitate SoEM data analysis for researchers who may not have advanced bioinformatics skills. Results: We demonstrated the capabilities of SoEM-Web by reanalyzing previously published datasets. This reanalysis not only confirmed the utility of the platform but also revealed additional taxa, emphasizing the value of updated reference datasets. The application successfully simplifies complex bioinformatics processes, enhancing accessibility and reproducibility in marine microeukaryote diversity research. SoEM-Web aims to enhance accessibility and reproducibility in marine microeukaryote diversity research. The web server is freely available at http://compsysbio.re.kr/soem-web/.Competing Interest StatementThe authors have declared no competing interest. | |
| 653 | |a Data processing | ||
| 653 | |a Marine ecosystems | ||
| 653 | |a Biogeochemical cycles | ||
| 653 | |a Biodiversity | ||
| 653 | |a Bioinformatics | ||
| 653 | |a Visualization | ||
| 653 | |a Metagenomics | ||
| 653 | |a Reproducibility | ||
| 700 | 1 | |a Kim, Hanjin | |
| 700 | 1 | |a Park, Chungoo | |
| 773 | 0 | |t bioRxiv |g (Feb 16, 2025) | |
| 786 | 0 | |d ProQuest |t Biological Science Database | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/3167424025/abstract/embedded/L8HZQI7Z43R0LA5T?source=fedsrch |
| 856 | 4 | 0 | |3 Full text outside of ProQuest |u https://www.biorxiv.org/content/10.1101/2025.02.12.637736v1 |