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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparison of genome sequencing technology and assembly methods for the analysis of a GC-rich bacterial genome</title><author><name sortKey="Scott, Derrick" sort="Scott, Derrick" uniqKey="Scott D" first="Derrick" last="Scott">Derrick Scott</name></author><author><name sortKey="Ely, Bert" sort="Ely, Bert" uniqKey="Ely B" first="Bert" last="Ely">Bert Ely</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25377284</idno><idno type="pmc">4318750</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4318750</idno><idno type="RBID">PMC:4318750</idno><idno type="doi">10.1007/s00284-014-0721-6</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000450</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparison of genome sequencing technology and assembly methods for the analysis of a GC-rich bacterial genome</title><author><name sortKey="Scott, Derrick" sort="Scott, Derrick" uniqKey="Scott D" first="Derrick" last="Scott">Derrick Scott</name></author><author><name sortKey="Ely, Bert" sort="Ely, Bert" uniqKey="Ely B" first="Bert" last="Ely">Bert Ely</name></author></analytic><series><title level="j">Current microbiology</title><idno type="ISSN">0343-8651</idno><idno type="eISSN">1432-0991</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec id="S1"><title>Motivation</title><p id="P1">Improvements in technology and decreases in price have made <italic>de novo</italic> bacterial genomic sequencing a reality for many researchers, but it has created a need to evaluate the methods for generating a complete and accurate genome assembly.</p></sec><sec id="S2"><title>Results</title><p id="P2">We sequenced the GC-rich <italic>Caulobacter henricii</italic> genome using the Illumina MiSeq, Roche 454, and Pacific Biosciences RS II sequencing systems. To generate a complete genome sequence, we performed assemblies using eight readily available programs and found that builds using the Illumina MiSeq and the Roche 454 data produced accurate yet numerous contigs. SPAdes performed the best followed by PANDAseq. In contrast, the Celera Assembler produced a single genomic contig using the Pacific Biosciences data after error correction with the Illumina MiSeq data. In addition, we duplicated this build using the Pacific Biosciences data with HGAP2.0. The accuracy of these builds was verified by Pulsed Field Gel Electrophoresis of genomic DNA cut with restriction enzymes.</p></sec></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
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<front><journal-meta><journal-id journal-id-type="nlm-journal-id">7808448</journal-id><journal-id journal-id-type="pubmed-jr-id">2282</journal-id><journal-id journal-id-type="nlm-ta">Curr Microbiol</journal-id><journal-id journal-id-type="iso-abbrev">Curr. Microbiol.</journal-id><journal-title-group><journal-title>Current microbiology</journal-title></journal-title-group><issn pub-type="ppub">0343-8651</issn><issn pub-type="epub">1432-0991</issn></journal-meta><article-meta><article-id pub-id-type="pmid">25377284</article-id><article-id pub-id-type="pmc">4318750</article-id><article-id pub-id-type="doi">10.1007/s00284-014-0721-6</article-id><article-id pub-id-type="manuscript">NIHMS641010</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Comparison of genome sequencing technology and assembly methods for the analysis of a GC-rich bacterial genome</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Scott</surname><given-names>Derrick</given-names></name><xref ref-type="corresp" rid="cor1">*</xref></contrib><contrib contrib-type="author"><name><surname>Ely</surname><given-names>Bert</given-names></name></contrib><aff id="A1">Department of Biological Sciences University of South Carolina Columbia SC 29208, USA</aff></contrib-group><author-notes><corresp id="cor1"><label>*</label>To whom correspondence should be addressed: Derrick Scott - <email>scottdc@mailbox.sc.edu</email></corresp></author-notes><pub-date pub-type="nihms-submitted"><day>9</day><month>11</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>07</day><month>11</month><year>2014</year></pub-date><pub-date pub-type="ppub"><month>3</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>01</day><month>3</month><year>2016</year></pub-date><volume>70</volume><issue>3</issue><fpage>338</fpage><lpage>344</lpage><pmc-comment>elocation-id from pubmed: 10.1007/s00284-014-0721-6</pmc-comment>
<abstract><sec id="S1"><title>Motivation</title><p id="P1">Improvements in technology and decreases in price have made <italic>de novo</italic> bacterial genomic sequencing a reality for many researchers, but it has created a need to evaluate the methods for generating a complete and accurate genome assembly.</p></sec><sec id="S2"><title>Results</title><p id="P2">We sequenced the GC-rich <italic>Caulobacter henricii</italic> genome using the Illumina MiSeq, Roche 454, and Pacific Biosciences RS II sequencing systems. To generate a complete genome sequence, we performed assemblies using eight readily available programs and found that builds using the Illumina MiSeq and the Roche 454 data produced accurate yet numerous contigs. SPAdes performed the best followed by PANDAseq. In contrast, the Celera Assembler produced a single genomic contig using the Pacific Biosciences data after error correction with the Illumina MiSeq data. In addition, we duplicated this build using the Pacific Biosciences data with HGAP2.0. The accuracy of these builds was verified by Pulsed Field Gel Electrophoresis of genomic DNA cut with restriction enzymes.</p></sec></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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