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Results: 1 to 20 of 112

1.

Reducing assembly complexity of microbial genomes with single-molecule sequencing.

Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM.

Genome Biol. 2013;14(9):R101.

PMID:
24034426
[PubMed - in process]
Free PMC Article
2.

Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology.

English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA.

PLoS One. 2012;7(11):e47768. doi: 10.1371/journal.pone.0047768. Epub 2012 Nov 21.

PMID:
23185243
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information.

Boetzer M, Pirovano W.

BMC Bioinformatics. 2014 Jun 20;15:211. doi: 10.1186/1471-2105-15-211.

PMID:
24950923
[PubMed - in process]
Free PMC Article
4.

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome.

Ferrarini M, Moretto M, Ward JA, Šurbanovski N, Stevanović V, Giongo L, Viola R, Cavalieri D, Velasco R, Cestaro A, Sargent DJ.

BMC Genomics. 2013 Oct 1;14:670. doi: 10.1186/1471-2164-14-670.

PMID:
24083400
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies.

Wetzel J, Kingsford C, Pop M.

BMC Bioinformatics. 2011 Apr 13;12:95. doi: 10.1186/1471-2105-12-95.

PMID:
21486487
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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
7.

Efficient and accurate whole genome assembly and methylome profiling of E. coli.

Powers JG, Weigman VJ, Shu J, Pufky JM, Cox D, Hurban P.

BMC Genomics. 2013 Oct 3;14:675. doi: 10.1186/1471-2164-14-675.

PMID:
24090403
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Adam M Phillippy.

Nat Biotechnol. 2012 Jul 1;30(7):693-700. doi: 10.1038/nbt.2280.

PMID:
22750884
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Reconstructing complex regions of genomes using long-read sequencing technology.

Huddleston J, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, Sudmant PH, Graves TA, Alkan C, Dennis MY, Wilson RK, Turner SW, Korlach J, Eichler EE.

Genome Res. 2014 Apr;24(4):688-96. doi: 10.1101/gr.168450.113. Epub 2014 Jan 13.

PMID:
24418700
[PubMed - in process]
10.

Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes.

Miyamoto M, Motooka D, Gotoh K, Imai T, Yoshitake K, Goto N, Iida T, Yasunaga T, Horii T, Arakawa K, Kasahara M, Nakamura S.

BMC Genomics. 2014 Aug 21;15:699. doi: 10.1186/1471-2164-15-699.

PMID:
25142801
[PubMed - in process]
Free PMC Article
11.

A hybrid approach for the automated finishing of bacterial genomes.

Bashir A, Klammer AA, Robins WP, Chin CS, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, Mollova E, Luong K, Lin S, LaMay B, Joshi A, Rowe L, Frace M, Tarr CL, Turnsek M, Davis BM, Kasarskis A, Mekalanos JJ, Waldor MK, Schadt EE.

Nat Biotechnol. 2012 Jul 1;30(7):701-7. doi: 10.1038/nbt.2288.

PMID:
22750883
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
13.

454 sequencing put to the test using the complex genome of barley.

Wicker T, Schlagenhauf E, Graner A, Close TJ, Keller B, Stein N.

BMC Genomics. 2006 Oct 26;7:275.

PMID:
17067373
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Whole-genome sequencing and assembly with high-throughput, short-read technologies.

Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S.

PLoS One. 2007 May 30;2(5):e484.

PMID:
17534434
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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]
16.

Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome.

Philippe R, Choulet F, Paux E, van Oeveren J, Tang J, Wittenberg AH, Janssen A, van Eijk MJ, Stormo K, Alberti A, Wincker P, Akhunov E, van der Vossen E, Feuillet C.

BMC Genomics. 2012 Jan 30;13:47. doi: 10.1186/1471-2164-13-47.

PMID:
22289472
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

SeqEntropy: genome-wide assessment of repeats for short read sequencing.

Chu HT, Hsiao WW, Tsao TT, Hsu DF, Chen CC, Lee SA, Kao CY.

PLoS One. 2013;8(3):e59484. doi: 10.1371/journal.pone.0059484. Epub 2013 Mar 27.

PMID:
23544073
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.

Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS.

BMC Genomics. 2008 Aug 28;9:404. doi: 10.1186/1471-2164-9-404.

PMID:
18755037
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data.

Desai A, Marwah VS, Yadav A, Jha V, Dhaygude K, Bangar U, Kulkarni V, Jere A.

PLoS One. 2013 Apr 12;8(4):e60204. doi: 10.1371/journal.pone.0060204. Print 2013.

PMID:
23593174
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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

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