{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T04:48:37Z","timestamp":1774932517471,"version":"3.50.1"},"reference-count":0,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T00:00:00Z","timestamp":1774915200000},"content-version":"am","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Ancient DNA (aDNA) sequences present unique challenges for taxonomic classification due to extreme fragmentation (reads 20\u2013100\u2009bp), end-biased cytosine deamination, and high contamination rates. Conventional metagenomic classifiers based on exact k-mer matching or alignment lose discriminative power on such short and damaged reads, limiting the analysis of paleogenomic samples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present FALCON2, a compression-based metagenomic classifier that leverages position-aware finite-context models to maintain high accuracy on degraded viral ancient viruses. FALCON2 consolidates the capabilities of its predecessor, FALCON-meta, into a unified executable with enhanced features including model persistence, direct processing of compressed inputs, multiple file handling, and optional pre-filtering methodologies for contaminated samples. Under controlled benchmarking with database, taxonomy, and thread parity on simulated viral datasets, FALCON2 achieved an Area Under the Curve of Receiver Operating Characteristic (AUC-ROC) of 0.999, an Area Under Precision-Recall Curve (AUPRC) of 0.968, and an F1-score of 0.918, substantially outperforming Centrifuge (AUPRC\u2009=\u20090.625), Kraken2 (AUPRC\u2009=\u20090.184), and CLARK-S (AUPRC\u2009=\u20090.013) on pooled micro-averaged metrics. FALCON2\u2019s advantage is most pronounced on ultra-short reads (20\u201340\u2009bp), where exact k-mers become sparse. FALCON2 pre-filtering at threshold 0.7 improved precision by 10 percentage points with negligible recall loss. FALCON2 runs on systems with 4\u20138\u2009GB RAM for typical analyses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>FALCON2 is freely available at https:\/\/github.com\/cobilab\/FALCON2 under GPL v3 license. Benchmarking data and scripts are archived at DOI: https:\/\/doi.org\/10.5281\/zenodo.17291214.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag155","type":"journal-article","created":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T12:40:57Z","timestamp":1774356057000},"source":"Crossref","is-referenced-by-count":0,"title":["FALCON2: compression-based metagenomic classification of ancient viruses"],"prefix":"10.1093","author":[{"given":"Luis L","family":"Marques","sequence":"first","affiliation":[{"name":"University of Aveiro IEETA\u2014Institute of Electronics and Informatics Engineering of Aveiro, ,","place":["Portugal"]},{"name":"University of Aveiro DETI\u2014Department of Electronics, Telecommunications and Informatics, ,","place":["Portugal"]},{"name":"University of Aveiro LASI\u2014Intelligent Systems Associate Laboratory, ,","place":["Portugal"]}]},{"given":"Armando J","family":"Pinho","sequence":"additional","affiliation":[{"name":"University of Aveiro IEETA\u2014Institute of Electronics and Informatics Engineering of Aveiro, ,","place":["Portugal"]},{"name":"University of Aveiro DETI\u2014Department of Electronics, Telecommunications and Informatics, ,","place":["Portugal"]},{"name":"University of Aveiro LASI\u2014Intelligent Systems Associate Laboratory, ,","place":["Portugal"]}]},{"given":"Diogo","family":"Pratas","sequence":"additional","affiliation":[{"name":"University of Aveiro IEETA\u2014Institute of Electronics and Informatics Engineering of Aveiro, ,","place":["Portugal"]},{"name":"University of Aveiro DETI\u2014Department of Electronics, Telecommunications and Informatics, ,","place":["Portugal"]},{"name":"University of Aveiro LASI\u2014Intelligent Systems Associate Laboratory, ,","place":["Portugal"]},{"name":"University of Helsinki DoV\u2014Department of Virology, ,","place":["Finland"]}]}],"member":"286","published-online":{"date-parts":[[2026,3,30]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag155\/67664575\/btag155.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag155\/67664575\/btag155.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T03:15:29Z","timestamp":1774926929000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/btag155\/8561075"}},"subtitle":[],"editor":[{"given":"Christina","family":"Kendziorski","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2026,3,30]]},"references-count":0,"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag155","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,30]]},"article-number":"btag155"}}