{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T17:29:14Z","timestamp":1785432554736,"version":"3.56.0"},"posted":{"date-parts":[[2025,7,18]]},"group-title":"Bioinformatics","reference-count":32,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,7,18]],"date-time":"2025-07-18T00:00:00Z","timestamp":1752796800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"award":["R01AI170111"],"award-info":[{"award-number":["R01AI170111"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,24]]},"abstract":"<jats:p>Functional profiling of meta-omics is essential for understanding microbial communities, yet support for custom genome-resolved reference databases is limited. We introduce Leviathan for integrated taxonomic and functional profiling at both genome and pangenome resolution. Leviathan combines Sylph for ultrafast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA-space against (pan)genome-resolved gene catalogs, producing dual metrics per (pan)genome: pathway abundance and graph-based pathway coverage. Benchmarking alignment backends on synthetic metagenomes, we show that DNA-space pseudo-alignments retain competitive (pan)genome-level classification performance compared to traditional alignment, reducing computational runtime and memory requirements, while translated searches in protein-space lose classification resolution from ambiguous mapping events. Leviathan's utility is demonstrated through two case studies: a marine plastisphere metagenomics dataset analyzing metabolic shifts between early and mature biofilm communities and a dental caries metatranscriptomics dataset where co-expression network analysis identified organism-specific transcriptional patterns diagnostic of health and disease states. Leviathan is available at https:\/\/github.com\/jolespin\/leviathan.<\/jats:p>","DOI":"10.1101\/2025.07.14.664802","type":"posted-content","created":{"date-parts":[[2025,7,18]],"date-time":"2025-07-18T23:40:15Z","timestamp":1752882015000},"source":"Crossref","is-referenced-by-count":0,"title":["Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for (pan)genome-resolved metagenomics and metatranscriptomics"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3447-3845","authenticated-orcid":false,"given":"Josh L","family":"Espinoza","sequence":"first","affiliation":[{"name":"J. 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