Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 266

1.

Fine de novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40.

Umemura M, Koyama Y, Takeda I, Hagiwara H, Ikegami T, Koike H, Machida M.

PLoS One. 2013 May 7;8(5):e63673. doi: 10.1371/journal.pone.0063673. Print 2013.

2.

Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data.

Ikegami T, Inatsugi T, Kojima I, Umemura M, Hagiwara H, Machida M, Asai K.

PLoS One. 2015 Apr 28;10(4):e0126289. doi: 10.1371/journal.pone.0126289. eCollection 2015.

3.

Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology.

Ruan J, Jiang L, Chong Z, Gong Q, Li H, Li C, Tao Y, Zheng C, Zhai W, Turissini D, Cannon CH, Lu X, Wu CI.

BMC Genomics. 2013 Oct 17;14:711. doi: 10.1186/1471-2164-14-711.

4.

Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing.

Chen TW, Gan RC, Chang YF, Liao WC, Wu TH, Lee CC, Huang PJ, Lee CY, Chen YY, Chiu CH, Tang P.

BMC Genomics. 2015 Aug 28;16:648. doi: 10.1186/s12864-015-1859-8.

5.

De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.

Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, Halliday K, Kamerewerd J, Kempken F, Knab B, Kuo HC, Osiewacz HD, Pöggeler S, Read ND, Seiler S, Smith KM, Zickler D, Kück U, Freitag M.

PLoS Genet. 2010 Apr 8;6(4):e1000891. doi: 10.1371/journal.pgen.1000891.

6.

Comparative genome analysis between Aspergillus oryzae strains reveals close relationship between sites of mutation localization and regions of highly divergent genes among Aspergillus species.

Umemura M, Koike H, Yamane N, Koyama Y, Satou Y, Kikuzato I, Teruya M, Tsukahara M, Imada Y, Wachi Y, Miwa Y, Yano S, Tamano K, Kawarabayasi Y, Fujimori KE, Machida M, Hirano T.

DNA Res. 2012 Oct;19(5):375-82. doi: 10.1093/dnares/dss019. Epub 2012 Aug 21.

7.

Paired-end sequencing of long-range DNA fragments for de novo assembly of large, complex Mammalian genomes by direct intra-molecule ligation.

Asan, Geng C, Chen Y, Wu K, Cai Q, Wang Y, Lang Y, Cao H, Yang H, Wang J, Zhang X.

PLoS One. 2012;7(9):e46211. doi: 10.1371/journal.pone.0046211. Epub 2012 Sep 27.

8.

SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome.

Stadermann KB, Weisshaar B, Holtgräwe D.

BMC Bioinformatics. 2015 Sep 16;16:295. doi: 10.1186/s12859-015-0726-6.

9.

The complex task of choosing a de novo assembly: lessons from fungal genomes.

Gallo JE, Muñoz JF, Misas E, McEwen JG, Clay OK.

Comput Biol Chem. 2014 Dec;53 Pt A:97-107. doi: 10.1016/j.compbiolchem.2014.08.014. Epub 2014 Aug 29.

PMID:
25262360
10.

Software for pre-processing Illumina next-generation sequencing short read sequences.

Chen C, Khaleel SS, Huang H, Wu CH.

Source Code Biol Med. 2014 May 3;9:8. doi: 10.1186/1751-0473-9-8. eCollection 2014.

11.

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.

12.
13.

A biologist's guide to de novo genome assembly using next-generation sequence data: A test with fungal genomes.

Haridas S, Breuill C, Bohlmann J, Hsiang T.

J Microbiol Methods. 2011 Sep;86(3):368-75. doi: 10.1016/j.mimet.2011.06.019. Epub 2011 Jul 3.

PMID:
21749903
14.

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.

15.

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.

16.

De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae.

Reinhardt JA, Baltrus DA, Nishimura MT, Jeck WR, Jones CD, Dangl JL.

Genome Res. 2009 Feb;19(2):294-305. doi: 10.1101/gr.083311.108. Epub 2008 Nov 17.

17.

De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.

Olsen RA, Bunikis I, Tiukova I, Holmberg K, Lötstedt B, Pettersson OV, Passoth V, Käller M, Vezzi F.

Gigascience. 2015 Nov 26;4:56. doi: 10.1186/s13742-015-0094-1. eCollection 2015.

18.

Meraculous: de novo genome assembly with short paired-end reads.

Chapman JA, Ho I, Sunkara S, Luo S, Schroth GP, Rokhsar DS.

PLoS One. 2011;6(8):e23501. doi: 10.1371/journal.pone.0023501. Epub 2011 Aug 18.

19.

The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads.

Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, Lambert G, Galbraith DW, Grassa CJ, Geraldes A, Cronk QC, Cullis C, Dash PK, Kumar PA, Cloutier S, Sharpe AG, Wong GK, Wang J, Deyholos MK.

Plant J. 2012 Nov;72(3):461-73. doi: 10.1111/j.1365-313X.2012.05093.x. Epub 2012 Aug 14.

20.

HGA: de novo genome assembly method for bacterial genomes using high coverage short sequencing reads.

Al-Okaily AA.

BMC Genomics. 2016 Mar 5;17:193. doi: 10.1186/s12864-016-2515-7.

Supplemental Content

Support Center