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Items: 1 to 20 of 168

1.

Aggressive assembly of pyrosequencing reads with mates.

Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G.

Bioinformatics. 2008 Dec 15;24(24):2818-24. doi: 10.1093/bioinformatics/btn548. Epub 2008 Oct 24.

2.

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.

3.

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. Epub 2013 Aug 29.

4.

QuorUM: An Error Corrector for Illumina Reads.

Marçais G, Yorke JA, Zimin A.

PLoS One. 2015 Jun 17;10(6):e0130821. doi: 10.1371/journal.pone.0130821. eCollection 2015.

5.

Omega: an overlap-graph de novo assembler for metagenomics.

Haider B, Ahn TH, Bushnell B, Chai J, Copeland A, Pan C.

Bioinformatics. 2014 Oct;30(19):2717-22. doi: 10.1093/bioinformatics/btu395. Epub 2014 Jun 19.

PMID:
24947750
6.

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.

7.

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. eCollection 2015.

8.

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.

9.

Crystallizing short-read assemblies around seeds.

Hossain MS, Azimi N, Skiena S.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S16. doi: 10.1186/1471-2105-10-S1-S16.

10.

A de novo metagenomic assembly program for shotgun DNA reads.

Lai B, Ding R, Li Y, Duan L, Zhu H.

Bioinformatics. 2012 Jun 1;28(11):1455-62. doi: 10.1093/bioinformatics/bts162. Epub 2012 Apr 11.

PMID:
22495746
11.

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.

Boisvert S, Laviolette F, Corbeil J.

J Comput Biol. 2010 Nov;17(11):1519-33. doi: 10.1089/cmb.2009.0238. Epub 2010 Oct 20.

12.

ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly.

Silver DH, Ben-Elazar S, Bogoslavsky A, Yanai I.

Bioinformatics. 2013 Jun 1;29(11):1455-7. doi: 10.1093/bioinformatics/btt169. Epub 2013 Apr 19.

PMID:
23603334
13.

Subset selection of high-depth next generation sequencing reads for de novo genome assembly using MapReduce framework.

Fang CH, Chang YJ, Chung WC, Hsieh PH, Lin CY, Ho JM.

BMC Genomics. 2015;16 Suppl 12:S9. doi: 10.1186/1471-2164-16-S12-S9. Epub 2015 Dec 9.

14.

FLASH: fast length adjustment of short reads to improve genome assemblies.

Magoč T, Salzberg SL.

Bioinformatics. 2011 Nov 1;27(21):2957-63. doi: 10.1093/bioinformatics/btr507. Epub 2011 Sep 7.

15.

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.

16.

SOPRA: Scaffolding algorithm for paired reads via statistical optimization.

Dayarian A, Michael TP, Sengupta AM.

BMC Bioinformatics. 2010 Jun 24;11:345. doi: 10.1186/1471-2105-11-345.

17.

The phusion assembler.

Mullikin JC, Ning Z.

Genome Res. 2003 Jan;13(1):81-90.

18.

ABySS: a parallel assembler for short read sequence data.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.

Genome Res. 2009 Jun;19(6):1117-23. doi: 10.1101/gr.089532.108. Epub 2009 Feb 27.

19.

Misassembly detection using paired-end sequence reads and optical mapping data.

Muggli MD, Puglisi SJ, Ronen R, Boucher C.

Bioinformatics. 2015 Jun 15;31(12):i80-8. doi: 10.1093/bioinformatics/btv262.

20.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

Kisand V, Lettieri T.

BMC Genomics. 2013 Apr 1;14:211. doi: 10.1186/1471-2164-14-211.

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