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Results: 1 to 20 of 100

1.

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
2.

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.

Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M.

Brief Bioinform. 2013 Mar;14(2):213-24. doi: 10.1093/bib/bbr074. Epub 2011 Dec 23.

PMID:
22199379
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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
4.

OSLay: optimal syntenic layout of unfinished assemblies.

Richter DC, Schuster SC, Huson DH.

Bioinformatics. 2007 Jul 1;23(13):1573-9. Epub 2007 Apr 26.

PMID:
17463020
[PubMed - indexed for MEDLINE]
Free Article
5.

Figaro: a novel statistical method for vector sequence removal.

White JR, Roberts M, Yorke JA, Pop M.

Bioinformatics. 2008 Feb 15;24(4):462-7. doi: 10.1093/bioinformatics/btm632. Epub 2008 Jan 17.

PMID:
18202027
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

ReDiT: Repeat Discrepancy Tagger--a shotgun assembly finishing aid.

Tammi MT, Arner E, Kindlund E, Andersson B.

Bioinformatics. 2004 Mar 22;20(5):803-4. Epub 2004 Jan 29.

PMID:
14751967
[PubMed - indexed for MEDLINE]
Free Article
7.

SEWAL: an open-source platform for next-generation sequence analysis and visualization.

Pitt JN, Rajapakse I, Ferré-D'Amaré AR.

Nucleic Acids Res. 2010 Dec;38(22):7908-15. doi: 10.1093/nar/gkq661. Epub 2010 Aug 6.

PMID:
20693400
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

EagleView: a genome assembly viewer for next-generation sequencing technologies.

Huang W, Marth G.

Genome Res. 2008 Sep;18(9):1538-43. doi: 10.1101/gr.076067.108. Epub 2008 Jun 11.

PMID:
18550804
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

ABACAS: algorithm-based automatic contiguation of assembled sequences.

Assefa S, Keane TM, Otto TD, Newbold C, Berriman M.

Bioinformatics. 2009 Aug 1;25(15):1968-9. doi: 10.1093/bioinformatics/btp347. Epub 2009 Jun 3.

PMID:
19497936
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Minimus: a fast, lightweight genome assembler.

Sommer DD, Delcher AL, Salzberg SL, Pop M.

BMC Bioinformatics. 2007 Feb 26;8:64.

PMID:
17324286
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

VIRS: A visual tool for identifying restriction sites in multiple DNA sequences.

Chen X, Luo C, Ma X, Chen M.

Biotechnol Prog. 2009 Sep-Oct;25(5):1525-7. doi: 10.1002/btpr.259.

PMID:
19637395
[PubMed - indexed for MEDLINE]
12.

GATA: a graphic alignment tool for comparative sequence analysis.

Nix DA, Eisen MB.

BMC Bioinformatics. 2005 Jan 17;6:9.

PMID:
15655071
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
18952627
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.

Bartels D, Kespohl S, Albaum S, Drüke T, Goesmann A, Herold J, Kaiser O, Pühler A, Pfeiffer F, Raddatz G, Stoye J, Meyer F, Schuster SC.

Bioinformatics. 2005 Apr 1;21(7):853-9. Epub 2004 Oct 28.

PMID:
15514001
[PubMed - indexed for MEDLINE]
Free Article
15.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ.

BMC Genomics. 2012 Apr 5;13:131. doi: 10.1186/1471-2164-13-131.

PMID:
22480257
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Plantagora: modeling whole genome sequencing and assembly of plant genomes.

Barthelson R, McFarlin AJ, Rounsley SD, Young S.

PLoS One. 2011;6(12):e28436. doi: 10.1371/journal.pone.0028436. Epub 2011 Dec 12.

PMID:
22174807
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

SEQuel: improving the accuracy of genome assemblies.

Ronen R, Boucher C, Chitsaz H, Pevzner P.

Bioinformatics. 2012 Jun 15;28(12):i188-96. doi: 10.1093/bioinformatics/bts219.

PMID:
22689760
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

preAssemble: a tool for automatic sequencer trace data processing.

Adzhubei AA, Laerdahl JK, Vlasova AV.

BMC Bioinformatics. 2006 Jan 17;7:22.

PMID:
16417643
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
21559467
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware.

Shi H, Schmidt B, Liu W, Müller-Wittig W.

J Comput Biol. 2010 Apr;17(4):603-15. doi: 10.1089/cmb.2009.0062.

PMID:
20426693
[PubMed - indexed for MEDLINE]

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