{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T12:38:48Z","timestamp":1773146328833,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2314,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data.<\/jats:p>\n               <jats:p>Results: We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes.<\/jats:p>\n               <jats:p>Availability and implementation: The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http:\/\/nbase.biology.gatech.edu\/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems.<\/jats:p>\n               <jats:p>Contact: \u00a0king.jordan@biology.gatech.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq284","type":"journal-article","created":{"date-parts":[[2010,6,3]],"date-time":"2010-06-03T01:10:05Z","timestamp":1275527405000},"page":"1819-1826","source":"Crossref","is-referenced-by-count":64,"title":["A computational genomics pipeline for prokaryotic sequencing projects"],"prefix":"10.1093","volume":"26","author":[{"given":"Andrey O.","family":"Kislyuk","sequence":"first","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Lee S.","family":"Katz","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Sonia","family":"Agrawal","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Matthew S.","family":"Hagen","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Andrew B.","family":"Conley","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Pushkala","family":"Jayaraman","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Viswateja","family":"Nelakuditi","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Jay C.","family":"Humphrey","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Scott A.","family":"Sammons","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Dhwani","family":"Govil","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Raydel D.","family":"Mair","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Kathleen M.","family":"Tatti","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Maria L.","family":"Tondella","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Brian H.","family":"Harcourt","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"Leonard W.","family":"Mayer","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]},{"given":"I. King","family":"Jordan","sequence":"additional","affiliation":[{"name":"1 School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, 2Core Biotechnology Facility and 3Meningitis and Vaccine Preventable Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,6,2]]},"reference":[{"key":"2023012507581558300_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012507581558300_B2","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"2023012507581558300_B3","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1016\/j.jmb.2004.05.028","article-title":"Improved prediction of signal peptides: SignalP 3.0","volume":"340","author":"Bendtsen","year":"2004","journal-title":"J. Mol. Biol."},{"key":"2023012507581558300_B4","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/nature07517","article-title":"Accurate whole human genome sequencing using reversible terminator chemistry","volume":"456","author":"Bentley","year":"2008","journal-title":"Nature"},{"key":"2023012507581558300_B5","doi-asserted-by":"crossref","first-page":"2607","DOI":"10.1093\/nar\/29.12.2607","article-title":"GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions","volume":"29","author":"Besemer","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023012507581558300_B6","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/nar\/gkg095","article-title":"The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003","volume":"31","author":"Boeckmann","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012507581558300_B7","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/nrmicro844","article-title":"DNA uptake during bacterial transformation","volume":"2","author":"Chen","year":"2004","journal-title":"Nat. Rev. Microbiol."},{"key":"2023012507581558300_B8","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: a reference database for bacterial virulence factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012507581558300_B9","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: multiple alignment of conserved genomic sequence with rearrangements","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Res."},{"key":"2023012507581558300_B10","doi-asserted-by":"crossref","first-page":"4636","DOI":"10.1093\/nar\/27.23.4636","article-title":"Improved microbial gene identification with GLIMMER","volume":"27","author":"Delcher","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2023012507581558300_B11","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1126\/science.1162986","article-title":"Real-Time DNA Sequencing from single polymerase molecules","volume":"323","author":"Eid","year":"2009","journal-title":"Science"},{"key":"2023012507581558300_B12","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1126\/science.7542800","article-title":"Whole-genome random sequencing and assembly of Haemophilus influenzae Rd","volume":"269","author":"Fleischmann","year":"1995","journal-title":"Science"},{"key":"2023012507581558300_B13","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/S1286-4579(00)01353-8","article-title":"Evolutionary trends in the genus Bordetella","volume":"3","author":"Gerlach","year":"2001","journal-title":"Microbes Infect.\/Institut Pasteur"},{"key":"2023012507581558300_B14","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1093\/oxfordjournals.molbev.a026159","article-title":"The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis","volume":"16","author":"Holmes","year":"1999","journal-title":"Mol. Biol. Evol."},{"key":"2023012507581558300_B15","doi-asserted-by":"crossref","first-page":"3733","DOI":"10.1099\/mic.0.29261-0","article-title":"Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes","volume":"152","author":"Hotopp","year":"2006","journal-title":"Microbiology"},{"key":"2023012507581558300_B16","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1093\/molbev\/msi041","article-title":"The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis","volume":"22","author":"Jolley","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"2023012507581558300_B17","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1504\/IJBRA.2009.027519","article-title":"Frameshift detection in prokaryotic genomic sequences","volume":"5","author":"Kislyuk","year":"2009","journal-title":"Int. J. Bioinform. Res. Appl."},{"key":"2023012507581558300_B18","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden markov model: application to complete genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023012507581558300_B19","doi-asserted-by":"crossref","first-page":"12381","DOI":"10.1073\/pnas.95.21.12381","article-title":"Natural genetic exchange between Haemophilus and Neisseria: intergeneric transfer of chromosomal genes between major human pathogens","volume":"95","author":"Kroll","year":"1998","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012507581558300_B20","doi-asserted-by":"publisher","DOI":"10.1038\/npre.2009.3191.1","author":"Kuo","year":"2009","journal-title":"Challenges in whole-genome annotation of pyrosequenced fungal genomes."},{"key":"2023012507581558300_B21","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.tig.2008.12.004","article-title":"Estimating the size of the bacterial pan-genome","volume":"25","author":"Lapierre","year":"2009","journal-title":"Trends Genet."},{"key":"2023012507581558300_B22","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012507581558300_B23","doi-asserted-by":"crossref","first-page":"R103","DOI":"10.1186\/gb-2009-10-10-r103","article-title":"ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads","volume":"10","author":"MacCallum","year":"2009","journal-title":"Genome Biol."},{"key":"2023012507581558300_B24","doi-asserted-by":"crossref","first-page":"3140","DOI":"10.1073\/pnas.95.6.3140","article-title":"Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms","volume":"95","author":"Maiden","year":"1998","journal-title":"Proc. Natl Acad. Sci.USA"},{"key":"2023012507581558300_B25","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature03959","article-title":"Genome sequencing in microfabricated high-density picolitre reactors","volume":"437","author":"Margulies","year":"2005","journal-title":"Nature"},{"key":"2023012507581558300_B26","doi-asserted-by":"crossref","first-page":"D382","DOI":"10.1093\/nar\/gkp887","article-title":"The integrated microbial genomes system: an expanding comparative analysis resource","volume":"38","author":"Markowitz","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012507581558300_B27","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1098\/rspb.2003.2416","article-title":"Epidemiology, hypermutation, within-host evolution and the virulence of Neisseria meningitidis","volume":"270","author":"Meyers","year":"2003","journal-title":"Proc. Biol. Sci.\/Roy. Soc."},{"key":"2023012507581558300_B28","doi-asserted-by":"crossref","first-page":"2818","DOI":"10.1093\/bioinformatics\/btn548","article-title":"Aggressive assembly of pyrosequencing reads with mates","volume":"24","author":"Miller","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012507581558300_B29","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/978-1-59745-515-2_5","article-title":"InterPro and InterProScan: tools for protein sequence classification and comparison","volume":"396","author":"Mulder","year":"2007","journal-title":"Methods Mol. Biol."},{"key":"2023012507581558300_B30","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1038\/ng1227","article-title":"Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica","volume":"35","author":"Parkhill","year":"2003","journal-title":"Nat. Genet."},{"key":"2023012507581558300_B31","doi-asserted-by":"crossref","first-page":"7063","DOI":"10.1128\/IAI.70.12.7063-7072.2002","article-title":"Comparative genomics identifies the genetic islands that distinguish Neisseria meningitidis, the agent of cerebrospinal meningitis, from other Neisseria species","volume":"70","author":"Perrin","year":"2002","journal-title":"Infect. Immun."},{"key":"2023012507581558300_B32","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1093\/bib\/5.3.237","article-title":"Comparative genome assembly","volume":"5","author":"Pop","year":"2004","journal-title":"Brief Bioinform."},{"key":"2023012507581558300_B33","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/nmeth.1172","article-title":"Pyrobayes: an improved base caller for SNP discovery in pyrosequences","volume":"5","author":"Quinlan","year":"2008","journal-title":"Nat. Methods"},{"key":"2023012507581558300_B34","doi-asserted-by":"crossref","first-page":"2071","DOI":"10.1093\/bioinformatics\/btp356","article-title":"Reordering contigs of draft genomes using the Mauve Aligner","volume":"25","author":"Rissman","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012507581558300_B35","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1056\/NEJM200105033441807","article-title":"Meningococcal disease","volume":"344","author":"Rosenstein","year":"2001","journal-title":"N. Engl. J. Med."},{"key":"2023012507581558300_B36","doi-asserted-by":"crossref","first-page":"3473","DOI":"10.1073\/pnas.0800151105","article-title":"Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis","volume":"105","author":"Schoen","year":"2008","journal-title":"Proc. Natl Acad. Sci."},{"key":"2023012507581558300_B37","doi-asserted-by":"crossref","first-page":"e75","DOI":"10.1371\/journal.pbio.0050075","article-title":"CAMERA: a community resource for metagenomics","volume":"5","author":"Seshadri","year":"2007","journal-title":"PLoS Biol."},{"key":"2023012507581558300_B38","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.1126\/science.1117389","article-title":"Accurate multiplex polony sequencing of an evolved bacterial genome","volume":"309","author":"Shendure","year":"2005","journal-title":"Science"},{"key":"2023012507581558300_B39","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1186\/1471-2105-8-64","article-title":"Minimus: a fast, lightweight genome assembler","volume":"8","author":"Sommer","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023012507581558300_B40","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1093\/bioinformatics\/btp097","article-title":"DIYA: a bacterial annotation pipeline for any genomics lab","volume":"25","author":"Stewart","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012507581558300_B41","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial \u2018pan-genome\u2019","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012507581558300_B42","doi-asserted-by":"crossref","first-page":"D169","DOI":"10.1093\/nar\/gkn664","article-title":"The Universal Protein Resource (UniProt) 2009","volume":"37","author":"Uniprot Consortium","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012507581558300_B43","doi-asserted-by":"crossref","first-page":"D539","DOI":"10.1093\/nar\/gkm951","article-title":"VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics","volume":"36","author":"Yang","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012507581558300_B44","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/15\/1819\/48852615\/bioinformatics_26_15_1819.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/15\/1819\/48852615\/bioinformatics_26_15_1819.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:58:40Z","timestamp":1674633520000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/15\/1819\/188418"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,6,2]]},"references-count":44,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2010,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq284","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,8,1]]},"published":{"date-parts":[[2010,6,2]]}}}