{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T11:02:39Z","timestamp":1785409359494,"version":"3.56.0"},"posted":{"date-parts":[[2026,2,23]]},"group-title":"Bioinformatics","reference-count":26,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T00:00:00Z","timestamp":1771804800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006545","name":"National Institute on Minority Health and Health Disparities","doi-asserted-by":"crossref","award":["U54MD012388"],"award-info":[{"award-number":["U54MD012388"]}],"id":[{"id":"10.13039\/100006545","id-type":"DOI","asserted-by":"crossref"}]},{"award":["R01AI172924"],"award-info":[{"award-number":["R01AI172924"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R15AI156771"],"award-info":[{"award-number":["R15AI156771"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Colgate Award for Research Excellence"},{"name":"University of Maryland School of Dentistry INSPIRE Grant"},{"name":"University of Maryland School of Dentistry PhD program in Dental Biomedical Science"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,2,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>MetaTracer is a nucleotide alignment-based tool for metatranscriptomic analysis of complex bacterial communities that assigns sequence reads to both taxonomic groups and expressed genes in a single pass. Full nucleotide-level alignment improves accuracy relative to k-mer-based classifiers and preserves species-level resolution that is often lost in protein-based approaches. By retaining alignment coordinates and mapping reads directly to annotated genomic features, MetaTracer enables direct attribution of gene expression to specific microbial species. On simulated datasets, MetaTracer achieves high accuracy for both taxonomic and gene assignment. Applied to real dental plaque metatranscriptomic datasets, MetaTracer resolves species-specific transcriptional activity and detects reproducible differences in microbial gene expression between children with early childhood caries and healthy controls.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MetaTracer is implemented as a Python-based workflow wrapper (metatracer v0.1.0) that depends on the mtsv-tools core engine (v2.1.0), which is written in Rust. The required functionality is supported by the v2.1.0 release of mtsv-tools. Both packages are open source under the MIT license and are available at github.com\/FofanovLab\/metatracer and github.com\/FofanovLab\/mtsv-tools. Versioned releases are archived at Zenodo (DOI: 10.5281\/zenodo.18665766 and DOI: 10.5281\/zenodo.18718002). Installation is supported via Bioconda.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>\n                    <jats:email>Viacheslav.Fofanov@nau.edu<\/jats:email>\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.02.20.707109","type":"posted-content","created":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T16:30:18Z","timestamp":1771864218000},"source":"Crossref","is-referenced-by-count":0,"title":["MetaTracer: A nucleotide alignment-based framework for high-resolution taxonomic and transcript assignment in metatranscriptomic data"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5233-7383","authenticated-orcid":false,"given":"Tara N.","family":"Furstenau","sequence":"first","affiliation":[{"name":"School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1514-2242","authenticated-orcid":false,"given":"Isaac","family":"Shaffer","sequence":"additional","affiliation":[{"name":"School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8551-6078","authenticated-orcid":false,"given":"Kuei-Ling C.","family":"Hsu","sequence":"additional","affiliation":[{"name":"Department of Orthodontics and Pediatric Dentistry, School of Dentistry, University of Maryland, Baltimore, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3696-041X","authenticated-orcid":false,"given":"Talima","family":"Pearson","sequence":"additional","affiliation":[{"name":"Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5016-8694","authenticated-orcid":false,"given":"Robert K.","family":"Ernst","sequence":"additional","affiliation":[{"name":"Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viacheslav Y.","family":"Fofanov","sequence":"additional","affiliation":[{"name":"School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA"},{"name":"Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026022507250595000_2026.02.20.707109v1.1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.65088"},{"key":"2026022507250595000_2026.02.20.707109v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01688-w"},{"key":"2026022507250595000_2026.02.20.707109v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-021-01101-x"},{"key":"2026022507250595000_2026.02.20.707109v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3176"},{"key":"2026022507250595000_2026.02.20.707109v1.5","doi-asserted-by":"publisher","DOI":"10.1101\/2021.06.03.446934"},{"key":"2026022507250595000_2026.02.20.707109v1.6","doi-asserted-by":"publisher","DOI":"10.1002\/IMT2.107"},{"key":"2026022507250595000_2026.02.20.707109v1.7","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2015.72"},{"key":"2026022507250595000_2026.02.20.707109v1.8","doi-asserted-by":"crossref","unstructured":"Ferragina P , Manzini G. 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