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Results: 1 to 20 of 100

1.

REAPR: a universal tool for genome assembly evaluation.

Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD.

Genome Biol. 2013 May 27;14(5):R47. doi: 10.1186/gb-2013-14-5-r47.

PMID:
23710727
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
25192061
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
24955109
[PubMed]
Free PMC Article
4.

ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.

Clark SC, Egan R, Frazier PI, Wang Z.

Bioinformatics. 2013 Feb 15;29(4):435-43. doi: 10.1093/bioinformatics/bts723. Epub 2013 Jan 9.

PMID:
23303509
[PubMed - indexed for MEDLINE]
Free Article
5.

Reference-guided assembly of four diverse Arabidopsis thaliana genomes.

Schneeberger K, Ossowski S, Ott F, Klein JD, Wang X, Lanz C, Smith LM, Cao J, Fitz J, Warthmann N, Henz SR, Huson DH, Weigel D.

Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10249-54. doi: 10.1073/pnas.1107739108. Epub 2011 Jun 6.

PMID:
21646520
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Employing whole genome mapping for optimal de novo assembly of bacterial genomes.

Xavier BB, Sabirova J, Pieter M, Hernalsteens JP, de Greve H, Goossens H, Malhotra-Kumar S.

BMC Res Notes. 2014 Jul 30;7:484. doi: 10.1186/1756-0500-7-484.

PMID:
25077983
[PubMed - in process]
Free PMC Article
7.

Automated ensemble assembly and validation of microbial genomes.

Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM.

BMC Bioinformatics. 2014 May 3;15:126. doi: 10.1186/1471-2105-15-126.

PMID:
24884846
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms.

Haznedaroglu BZ, Reeves D, Rismani-Yazdi H, Peccia J.

BMC Bioinformatics. 2012 Jul 18;13:170. doi: 10.1186/1471-2105-13-170.

PMID:
22808927
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Hawkeye: an interactive visual analytics tool for genome assemblies.

Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL.

Genome Biol. 2007;8(3):R34.

PMID:
17349036
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

De novo assembly of highly diverse viral populations.

Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, Qu J, Ryan EM, Zody MC, Henn MR.

BMC Genomics. 2012 Sep 13;13:475. doi: 10.1186/1471-2164-13-475.

PMID:
22974120
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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
12.

Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences.

Utturkar SM, Klingeman DM, Land ML, Schadt CW, Doktycz MJ, Pelletier DA, Brown SD.

Bioinformatics. 2014 Jun 14. pii: btu391. [Epub ahead of print]

PMID:
24930142
[PubMed - as supplied by publisher]
Free Article
13.

High-quality draft assemblies of mammalian genomes from massively parallel sequence data.

Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8. doi: 10.1073/pnas.1017351108. Epub 2010 Dec 27.

PMID:
21187386
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies.

Ruperao P, Chan CK, Azam S, Karafiátová M, Hayashi S, Cížková J, Saxena RK, Simková H, Song C, Vrána J, Chitikineni A, Visendi P, Gaur PM, Millán T, Singh KB, Taran B, Wang J, Batley J, Doležel J, Varshney RK, Edwards D.

Plant Biotechnol J. 2014 Aug;12(6):778-86. doi: 10.1111/pbi.12182. Epub 2014 Apr 5.

PMID:
24702794
[PubMed - in process]
15.

De novo likelihood-based measures for comparing genome assemblies.

Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M.

BMC Res Notes. 2013 Aug 22;6:334. doi: 10.1186/1756-0500-6-334.

PMID:
23965294
[PubMed - in process]
Free PMC Article
16.

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
17.

Genome assembly forensics: finding the elusive mis-assembly.

Phillippy AM, Schatz MC, Pop M.

Genome Biol. 2008;9(3):R55. doi: 10.1186/gb-2008-9-3-r55. Epub 2008 Mar 14.

PMID:
18341692
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Assembly reconciliation.

Zimin AV, Smith DR, Sutton G, Yorke JA.

Bioinformatics. 2008 Jan 1;24(1):42-5. Epub 2007 Dec 5.

PMID:
18057021
[PubMed - indexed for MEDLINE]
Free Article
19.

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
20.

Finishing bacterial genome assemblies with Mix.

Soueidan H, Maurier F, Groppi A, Sirand-Pugnet P, Tardy F, Citti C, Dupuy V, Nikolski M.

BMC Bioinformatics. 2013;14 Suppl 15:S16. doi: 10.1186/1471-2105-14-S15-S16. Epub 2013 Oct 15.

PMID:
24564706
[PubMed - indexed for MEDLINE]
Free PMC Article

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