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Items: 1 to 20 of 332

1.

Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing.

Solares EA, Chakraborty M, Miller DE, Kalsow S, Hall K, Perera AG, Emerson JJ, Hawley RS.

G3 (Bethesda). 2018 Oct 3;8(10):3143-3154. doi: 10.1534/g3.118.200162.

2.

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer.

Istace B, Friedrich A, d'Agata L, Faye S, Payen E, Beluche O, Caradec C, Davidas S, Cruaud C, Liti G, Lemainque A, Engelen S, Wincker P, Schacherer J, Aury JM.

Gigascience. 2017 Feb 1;6(2):1-13. doi: 10.1093/gigascience/giw018.

3.

Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage.

Chakraborty M, Baldwin-Brown JG, Long AD, Emerson JJ.

Nucleic Acids Res. 2016 Nov 2;44(19):e147. Epub 2016 Jul 25.

4.

Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing.

Goldstein S, Beka L, Graf J, Klassen JL.

BMC Genomics. 2019 Jan 9;20(1):23. doi: 10.1186/s12864-018-5381-7.

5.

Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing.

Miller DE, Staber C, Zeitlinger J, Hawley RS.

G3 (Bethesda). 2018 Oct 3;8(10):3131-3141. doi: 10.1534/g3.118.200160.

6.

MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome.

Tyson JR, O'Neil NJ, Jain M, Olsen HE, Hieter P, Snutch TP.

Genome Res. 2018 Feb;28(2):266-274. doi: 10.1101/gr.221184.117. Epub 2017 Dec 22.

7.

Genomic Structural Variations Within Five Continental Populations of Drosophila melanogaster.

Long E, Evans C, Chaston J, Udall JA.

G3 (Bethesda). 2018 Oct 3;8(10):3247-3253. doi: 10.1534/g3.118.200631.

8.

Nanopore sequencing and assembly of a human genome with ultra-long reads.

Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M.

Nat Biotechnol. 2018 Apr;36(4):338-345. doi: 10.1038/nbt.4060. Epub 2018 Jan 29.

9.

Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements.

McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, Pushkarev D, Petrov DA, Fiston-Lavier AS.

PLoS One. 2014 Sep 4;9(9):e106689. doi: 10.1371/journal.pone.0106689. eCollection 2014.

10.

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.

11.

High precision genome sequencing of engineered Gluconobacter oxydans 621H by combining long nanopore and short accurate Illumina reads.

Kranz A, Vogel A, Degner U, Kiefler I, Bott M, Usadel B, Polen T.

J Biotechnol. 2017 Sep 20;258:197-205. doi: 10.1016/j.jbiotec.2017.04.016. Epub 2017 Apr 19.

PMID:
28433722
12.

Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D.

Salazar AN, Gorter de Vries AR, van den Broek M, Wijsman M, de la Torre Cortés P, Brickwedde A, Brouwers N, Daran JG, Abeel T.

FEMS Yeast Res. 2017 Nov 1;17(7). doi: 10.1093/femsyr/fox074.

13.

Genome assembly using Nanopore-guided long and error-free DNA reads.

Madoui MA, Engelen S, Cruaud C, Belser C, Bertrand L, Alberti A, Lemainque A, Wincker P, Aury JM.

BMC Genomics. 2015 Apr 20;16:327. doi: 10.1186/s12864-015-1519-z.

14.

Rapid de novo assembly of the European eel genome from nanopore sequencing reads.

Jansen HJ, Liem M, Jong-Raadsen SA, Dufour S, Weltzien FA, Swinkels W, Koelewijn A, Palstra AP, Pelster B, Spaink HP, Thillart GEVD, Dirks RP, Henkel CV.

Sci Rep. 2017 Aug 3;7(1):7213. doi: 10.1038/s41598-017-07650-6. Erratum in: Sci Rep. 2019 May 22;9(1):7911.

15.

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A.

Nat Methods. 2015 Aug;12(8):780-6. doi: 10.1038/nmeth.3454. Epub 2015 Jun 29.

16.

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

Card DC, Schield DR, Reyes-Velasco J, Fujita MK, Andrew AL, Oyler-McCance SJ, Fike JA, Tomback DF, Ruggiero RP, Castoe TA.

PLoS One. 2014 Sep 5;9(9):e106649. doi: 10.1371/journal.pone.0106649. eCollection 2014.

17.

Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly.

Tan MH, Austin CM, Hammer MP, Lee YP, Croft LJ, Gan HM.

Gigascience. 2018 Mar 1;7(3):1-6. doi: 10.1093/gigascience/gix137.

18.

Oxford Nanopore MinION Sequencing and Genome Assembly.

Lu H, Giordano F, Ning Z.

Genomics Proteomics Bioinformatics. 2016 Oct;14(5):265-279. doi: 10.1016/j.gpb.2016.05.004. Epub 2016 Sep 17. Review.

19.

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms.

Giordano F, Aigrain L, Quail MA, Coupland P, Bonfield JK, Davies RM, Tischler G, Jackson DK, Keane TM, Li J, Yue JX, Liti G, Durbin R, Ning Z.

Sci Rep. 2017 Jun 21;7(1):3935. doi: 10.1038/s41598-017-03996-z.

20.

Challenges and advances for transcriptome assembly in non-model species.

Ungaro A, Pech N, Martin JF, McCairns RJS, Mévy JP, Chappaz R, Gilles A.

PLoS One. 2017 Sep 20;12(9):e0185020. doi: 10.1371/journal.pone.0185020. eCollection 2017.

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