{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T13:33:40Z","timestamp":1793021620663,"version":"4.5.0"},"reference-count":45,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","award":["BT\/PR40261\/BTIS\/137\/55\/2023"],"award-info":[{"award-number":["BT\/PR40261\/BTIS\/137\/55\/2023"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology Resources"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Strain\u2010level identification of each microbe is crucial for understanding its role in the host. Most of the existing tools have primarily been evaluated on human metagenomic datasets, whereas the plant microbiome exhibits greater diversity and complexity and thus poses a challenge in the strain\u2010level resolution of individual microbes. In this study, we conducted a comprehensive benchmarking of available reference\u2010based tools for strain\u2010level resolution of the plant microbiome. We evaluated seven tools on various performance parameters, like computational requirements, F1\u2010score and relative abundances using synthetic datasets comprising microbes known to have strong associations with plants as well as real plant microbiome datasets. Our results demonstrated a better performance of StrainScan on the synthetic data, achieving higher F1\u2010score and more accurate relative abundance estimates as compared to other tools, but its performance declined gradually with increasing strain diversity. However, StrainGE and StrainScan exhibited competitive performance on real plant metagenome data. Overall, though StrainGE exhibited better performance, it was more computationally expensive. However, StrainScan performed better in detecting low\u2010abundance strains. Our findings suggest the comparative suitability of the available tools for the strain\u2010level analysis of plant metagenome data and highlight the need for the development of more efficient and accurate taxonomic classifiers capable of handling the complex plant metagenome data while maintaining computational efficiency.<\/jats:p>","DOI":"10.1111\/1755-0998.70197","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T05:24:48Z","timestamp":1788845088000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Benchmarking of Reference\u2010Based Tools for Strain\u2010Level Resolution of Plant Microbiome"],"prefix":"10.1111","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-1985-1380","authenticated-orcid":false,"given":"Rishav","family":"Sahil","sequence":"first","affiliation":[{"name":"Translational Genomics and Systems Biology Laboratory, School of Computational and Integrative Sciences Jawaharlal Nehru University  New Delhi India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7622-1083","authenticated-orcid":false,"given":"Mukesh","family":"Jain","sequence":"additional","affiliation":[{"name":"Translational Genomics and Systems Biology Laboratory, School of Computational and Integrative Sciences Jawaharlal Nehru University  New Delhi India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,7]]},"reference":[{"key":"e_1_2_13_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.micres.2019.02.001"},{"key":"e_1_2_13_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-02209-5"},{"key":"e_1_2_13_4_1","unstructured":"Andrews S.2010.FastQC: A Quality Control Tool for High Throughput Sequence 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