{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T12:55:26Z","timestamp":1768481726250,"version":"3.49.0"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2484,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Shotgun sequencing generates large numbers of short DNA reads from either an isolated organism or, in the case of metagenomics projects, from the aggregate genome of a microbial community. These reads are then assembled based on overlapping sequences into larger, contiguous sequences (contigs). The feasibility of assembly and the coverage achieved (reads per nucleotide or distinct sequence of nucleotides) depend on several factors: the number of reads sequenced, the read length and the relative abundances of their source genomes in the microbial community. A low coverage suggests that most of the genomic DNA in the sample has not been sequenced, but it is often difficult to estimate either the extent of the uncaptured diversity or the amount of additional sequencing that would be most efficacious. In this work, we regard a metagenome as a population of DNA fragments (bins), each of which may be covered by one or more reads. We employ a gamma distribution to model this bin population due to its flexibility and ease of use. When a gamma approximation can be found that adequately fits the data, we may estimate the number of bins that were not sequenced and that could potentially be revealed by additional sequencing. We evaluated the performance of this model using simulated metagenomes and demonstrate its applicability on three recent metagenomic datasets.<\/jats:p>\n               <jats:p>Contact: \u00a0sean.d.hooper@genpat.uu.se<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp687","type":"journal-article","created":{"date-parts":[[2009,12,15]],"date-time":"2009-12-15T02:19:50Z","timestamp":1260843590000},"page":"295-301","source":"Crossref","is-referenced-by-count":28,"title":["Estimating DNA coverage and abundance in metagenomes using a gamma approximation"],"prefix":"10.1093","volume":"26","author":[{"given":"Sean D.","family":"Hooper","sequence":"first","affiliation":[{"name":"1 Department of Energy Joint Genome Institute (DOE-JGI), Genome Biology Program, 2800 Mitchell Drive, Walnut Creek, CA 94598 and 2 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Dalevi","sequence":"additional","affiliation":[{"name":"1 Department of Energy Joint Genome Institute (DOE-JGI), Genome Biology Program, 2800 Mitchell Drive, Walnut Creek, CA 94598 and 2 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amrita","family":"Pati","sequence":"additional","affiliation":[{"name":"1 Department of Energy Joint Genome Institute (DOE-JGI), Genome Biology Program, 2800 Mitchell Drive, Walnut Creek, CA 94598 and 2 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Konstantinos","family":"Mavromatis","sequence":"additional","affiliation":[{"name":"1 Department of Energy Joint Genome Institute (DOE-JGI), Genome Biology Program, 2800 Mitchell Drive, Walnut Creek, CA 94598 and 2 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalia N.","family":"Ivanova","sequence":"additional","affiliation":[{"name":"1 Department of Energy Joint Genome Institute (DOE-JGI), Genome Biology Program, 2800 Mitchell Drive, Walnut Creek, CA 94598 and 2 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikos C.","family":"Kyrpides","sequence":"additional","affiliation":[{"name":"1 Department of Energy Joint Genome Institute (DOE-JGI), Genome Biology Program, 2800 Mitchell Drive, Walnut Creek, CA 94598 and 2 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,12,14]]},"reference":[{"key":"2023012510595186300_B1","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-6-41","article-title":"PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information","volume":"6","author":"Angly","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012510595186300_B2","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1093\/biomet\/45.1-2.59","article-title":"Simplified methods of fitting the truncated negative binomial distribution","volume":"45","author":"Brass","year":"1958","journal-title":"Biometrika"},{"key":"2023012510595186300_B3","doi-asserted-by":"crossref","first-page":"14250","DOI":"10.1073\/pnas.202488399","article-title":"Genomic analysis of uncultured marine viral communities","volume":"99","author":"Breitbart","year":"2002","journal-title":"Proc. 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