{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T21:18:53Z","timestamp":1774819133641,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T00:00:00Z","timestamp":1478131200000},"content-version":"vor","delay-in-days":766,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis.<\/jats:p>\n               <jats:p>Results: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic reads to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. The algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains.<\/jats:p>\n               <jats:p>Availability and Implementation: Sigma was implemented in C++ with source codes and binaries freely available at http:\/\/sigma.omicsbio.org .<\/jats:p>\n               <jats:p>Contact: \u00a0panc@ornl.gov<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu641","type":"journal-article","created":{"date-parts":[[2014,9,30]],"date-time":"2014-09-30T05:52:55Z","timestamp":1412056375000},"page":"170-177","source":"Crossref","is-referenced-by-count":95,"title":["Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance"],"prefix":"10.1093","volume":"31","author":[{"given":"Tae-Hyuk","family":"Ahn","sequence":"first","affiliation":[{"name":"Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juanjuan","family":"Chai","sequence":"additional","affiliation":[{"name":"Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chongle","family":"Pan","sequence":"additional","affiliation":[{"name":"Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,9,29]]},"reference":[{"key":"2023020116142356700_btu641-B1","doi-asserted-by":"crossref","first-page":"e48228","DOI":"10.1371\/journal.pone.0048228","article-title":"Genomic comparison of \n              Escherichia coli\n               O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2","volume":"7","author":"Ahmed","year":"2012","journal-title":"PLoS One"},{"key":"2023020116142356700_btu641-B2","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1038\/nmeth0511-367","article-title":"PhymmBL expanded: confidence scores, custom databases, parallelization and more","volume":"8","author":"Brady","year":"2011","journal-title":"Nat. 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