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Results: 1 to 20 of 95

1.

Finished bacterial genomes from shotgun sequence data.

Ribeiro FJ, Przybylski D, Yin S, Sharpe T, Gnerre S, Abouelleil A, Berlin AM, Montmayeur A, Shea TP, Walker BJ, Young SK, Russ C, Nusbaum C, MacCallum I, Jaffe DB.

Genome Res. 2012 Nov;22(11):2270-7. doi: 10.1101/gr.141515.112. Epub 2012 Jul 24.

PMID:
22829535
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Finishing genomes with limited resources: lessons from an ensemble of microbial genomes.

Nagarajan N, Cook C, Di Bonaventura M, Ge H, Richards A, Bishop-Lilly KA, DeSalle R, Read TD, Pop M.

BMC Genomics. 2010 Apr 16;11:242. doi: 10.1186/1471-2164-11-242.

PMID:
20398345
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J.

Nat Methods. 2013 Jun;10(6):563-9. doi: 10.1038/nmeth.2474. Epub 2013 May 5.

PMID:
23644548
[PubMed - indexed for MEDLINE]
4.

ALLPATHS: de novo assembly of whole-genome shotgun microreads.

Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB.

Genome Res. 2008 May;18(5):810-20. doi: 10.1101/gr.7337908. Epub 2008 Mar 13.

PMID:
18340039
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

MGView: an alignment and visualization tool to enhance gap closure of microbial genomes.

Herron-Olson L, Freeman J, Zhang Q, Retzel EF, Kapur V.

Nucleic Acids Res. 2003 Sep 1;31(17):e106.

PMID:
12930980
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

An algorithm for automated closure during assembly.

Koren S, Miller JR, Walenz BP, Sutton G.

BMC Bioinformatics. 2010 Sep 10;11:457. doi: 10.1186/1471-2105-11-457.

PMID:
20831800
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, Goodwin L, Woyke T, Lapidus A, Klenk HP, Cottingham RW, Kyrpides NC.

PLoS One. 2012;7(12):e48837. doi: 10.1371/journal.pone.0048837. Epub 2012 Dec 12.

PMID:
23251337
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies.

Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, Poulain J, Anthouard V, Scarpelli C, Artiguenave F, Wincker P.

BMC Genomics. 2008 Dec 16;9:603. doi: 10.1186/1471-2164-9-603.

PMID:
19087275
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA.

J Comput Biol. 2012 May;19(5):455-77. doi: 10.1089/cmb.2012.0021. Epub 2012 Apr 16.

PMID:
22506599
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Correcting base-assignment errors in repeat regions of shotgun assembly.

Zhi D, Keich U, Pevzner P, Heber S, Tang H.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar;4(1):54-64.

PMID:
17277413
[PubMed - indexed for MEDLINE]
11.

Sequencing of high G+C microbial genomes using the ultrafast pyrosequencing technology.

Schwientek P, Szczepanowski R, Rückert C, Stoye J, Pühler A.

J Biotechnol. 2011 Aug 20;155(1):68-77. doi: 10.1016/j.jbiotec.2011.04.010. Epub 2011 Apr 23.

PMID:
21536083
[PubMed - indexed for MEDLINE]
12.

Comparative genome assembly.

Pop M, Phillippy A, Delcher AL, Salzberg SL.

Brief Bioinform. 2004 Sep;5(3):237-48.

PMID:
15383210
[PubMed - indexed for MEDLINE]
Free Article
13.

Applying Shannon's information theory to bacterial and phage genomes and metagenomes.

Akhter S, Bailey BA, Salamon P, Aziz RK, Edwards RA.

Sci Rep. 2013;3:1033. doi: 10.1038/srep01033. Epub 2013 Jan 8.

PMID:
23301154
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

AMASS: a structured pattern matching approach to shotgun sequence assembly.

Kim S, Segre AM.

J Comput Biol. 1999 Summer;6(2):163-86.

PMID:
10421521
[PubMed - indexed for MEDLINE]
15.

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.

Fitzsimons MS, Novotny M, Lo CC, Dichosa AE, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, Wills PL, Parson-Quintana B, Chain PS, Detter JC, Lasken RS, Han CS.

Genome Res. 2013 May;23(5):878-88. doi: 10.1101/gr.142208.112. Epub 2013 Mar 14.

PMID:
23493677
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

One bacterial cell, one complete genome.

Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A, Wu D, McCutcheon JP, McDonald BR, Moran NA, Bristow J, Cheng JF.

PLoS One. 2010 Apr 23;5(4):e10314. doi: 10.1371/journal.pone.0010314.

PMID:
20428247
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes.

Goldberg SM, Johnson J, Busam D, Feldblyum T, Ferriera S, Friedman R, Halpern A, Khouri H, Kravitz SA, Lauro FM, Li K, Rogers YH, Strausberg R, Sutton G, Tallon L, Thomas T, Venter E, Frazier M, Venter JC.

Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11240-5. Epub 2006 Jul 13. Erratum in: Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):16057.

PMID:
16840556
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis.

Schbath S, Martin V, Zytnicki M, Fayolle J, Loux V, Gibrat JF.

J Comput Biol. 2012 Jun;19(6):796-813. doi: 10.1089/cmb.2012.0022. Epub 2012 Apr 16.

PMID:
22506536
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Scaffolding and validation of bacterial genome assemblies using optical restriction maps.

Nagarajan N, Read TD, Pop M.

Bioinformatics. 2008 May 15;24(10):1229-35. doi: 10.1093/bioinformatics/btn102. Epub 2008 Mar 20.

PMID:
18356192
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Construction of bacterial artificial chromosome libraries from the parasitic nematode Brugia malayi and physical mapping of the genome of its Wolbachia endosymbiont.

Foster JM, Kumar S, Ganatra MB, Kamal IH, Ware J, Ingram J, Pope-Chappell J, Guiliano D, Whitton C, Daub J, Blaxter ML, Slatko BE.

Int J Parasitol. 2004 May;34(6):733-46.

PMID:
15111095
[PubMed - indexed for MEDLINE]

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