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Items: 1 to 20 of 215

1.

GAGE: A critical evaluation of genome assemblies and assembly algorithms.

Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA.

Genome Res. 2012 Mar;22(3):557-67. doi: 10.1101/gr.131383.111. Erratum in: Genome Res. 2012 Jun;22(6):1196.

2.

GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers.

Jünemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D.

PLoS One. 2014 Sep 8;9(9):e107014. doi: 10.1371/journal.pone.0107014. Erratum in: PLoS One. 2015;10(3):e0118741.

3.

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.

4.

Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations.

García-López R, Vázquez-Castellanos JF, Moya A.

Front Bioeng Biotechnol. 2015 Sep 17;3:141. doi: 10.3389/fbioe.2015.00141.

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.

6.

GAGE-B: an evaluation of genome assemblers for bacterial organisms.

Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, Salzberg SL.

Bioinformatics. 2013 Jul 15;29(14):1718-25. doi: 10.1093/bioinformatics/btt273.

7.

Efficient de novo assembly of large genomes using compressed data structures.

Simpson JT, Durbin R.

Genome Res. 2012 Mar;22(3):549-56. doi: 10.1101/gr.126953.111.

8.

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.

9.

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.

10.

Comparing de novo genome assembly: the long and short of it.

Narzisi G, Mishra B.

PLoS One. 2011 Apr 29;6(4):e19175. doi: 10.1371/journal.pone.0019175.

11.

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.

12.

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.

13.

The MaSuRCA genome assembler.

Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA.

Bioinformatics. 2013 Nov 1;29(21):2669-77. doi: 10.1093/bioinformatics/btt476.

14.

Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons.

Vezzi F, Narzisi G, Mishra B.

PLoS One. 2012;7(12):e52210. doi: 10.1371/journal.pone.0052210.

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.

16.

Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction.

Palmer LE, Dejori M, Bolanos R, Fasulo D.

BMC Bioinformatics. 2010 Jan 15;11:33. doi: 10.1186/1471-2105-11-33.

17.

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.

18.

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 Oct;30(19):2709-16. doi: 10.1093/bioinformatics/btu391.

19.

GAM-NGS: genomic assemblies merger for next generation sequencing.

Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A.

BMC Bioinformatics. 2013;14 Suppl 7:S6. doi: 10.1186/1471-2105-14-S7-S6.

20.

Benchmarking of de novo assembly algorithms for Nanopore data reveals optimal performance of OLC approaches.

Cherukuri Y, Janga SC.

BMC Genomics. 2016 Aug 22;17 Suppl 7:507. doi: 10.1186/s12864-016-2895-8.

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