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Results: 16

References for PMC Articles for PubMed (Select 22723971)

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. Epub 2012 Jan 6. Erratum in: Genome Res. 2012 Jun;22(6):1196.

2.

A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.

Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B.

PLoS One. 2011 Mar 14;6(3):e17915. doi: 10.1371/journal.pone.0017915.

3.

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.

Marçais G, Kingsford C.

Bioinformatics. 2011 Mar 15;27(6):764-70. doi: 10.1093/bioinformatics/btr011. Epub 2011 Jan 7.

4.

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.

5.

Scaffolding pre-assembled contigs using SSPACE.

Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W.

Bioinformatics. 2011 Feb 15;27(4):578-9. doi: 10.1093/bioinformatics/btq683. Epub 2010 Dec 12.

6.

Quake: quality-aware detection and correction of sequencing errors.

Kelley DR, Schatz MC, Salzberg SL.

Genome Biol. 2010;11(11):R116. doi: 10.1186/gb-2010-11-11-r116. Epub 2010 Nov 29.

7.

Assembly algorithms for next-generation sequencing data.

Miller JR, Koren S, Sutton G.

Genomics. 2010 Jun;95(6):315-27. doi: 10.1016/j.ygeno.2010.03.001. Epub 2010 Mar 6. Review.

8.

De novo assembly of human genomes with massively parallel short read sequencing.

Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J.

Genome Res. 2010 Feb;20(2):265-72. doi: 10.1101/gr.097261.109. Epub 2009 Dec 17.

9.

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.

10.

MetaSim: a sequencing simulator for genomics and metagenomics.

Richter DC, Ott F, Auch AF, Schmid R, Huson DH.

PLoS One. 2008 Oct 8;3(10):e3373. doi: 10.1371/journal.pone.0003373.

11.

Next-generation DNA sequencing methods.

Mardis ER.

Annu Rev Genomics Hum Genet. 2008;9:387-402. doi: 10.1146/annurev.genom.9.081307.164359. Review.

PMID:
18576944
12.

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Zerbino DR, Birney E.

Genome Res. 2008 May;18(5):821-9. doi: 10.1101/gr.074492.107. Epub 2008 Mar 18.

13.

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. Epub 2008 Mar 13.

14.

An Eulerian path approach to DNA fragment assembly.

Pevzner PA, Tang H, Waterman MS.

Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9748-53.

15.

A greedy algorithm for aligning DNA sequences.

Zhang Z, Schwartz S, Wagner L, Miller W.

J Comput Biol. 2000 Feb-Apr;7(1-2):203-14.

PMID:
10890397
16.

Identification of common molecular subsequences.

Smith TF, Waterman MS.

J Mol Biol. 1981 Mar 25;147(1):195-7. No abstract available.

PMID:
7265238
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