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Items: 1 to 20 of 32

1.

Reptile: representative tiling for short read error correction.

Yang X, Dorman KS, Aluru S.

Bioinformatics. 2010 Oct 15;26(20):2526-33. doi: 10.1093/bioinformatics/btq468. Epub 2010 Aug 16.

PMID:
20834037
2.

Correction of sequencing errors in a mixed set of reads.

Salmela L.

Bioinformatics. 2010 May 15;26(10):1284-90. doi: 10.1093/bioinformatics/btq151. Epub 2010 Apr 8.

PMID:
20378555
3.

Recount: expectation maximization based error correction tool for next generation sequencing data.

Wijaya E, Frith MC, Suzuki Y, Horton P.

Genome Inform. 2009 Oct;23(1):189-201.

4.

Fast and accurate long-read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2010 Mar 1;26(5):589-95. doi: 10.1093/bioinformatics/btp698. Epub 2010 Jan 15.

5.

Sequencing technologies - the next generation.

Metzker ML.

Nat Rev Genet. 2010 Jan;11(1):31-46. doi: 10.1038/nrg2626. Epub 2009 Dec 8. Review.

PMID:
19997069
6.

Improved base calling for the Illumina Genome Analyzer using machine learning strategies.

Kircher M, Stenzel U, Kelso J.

Genome Biol. 2009;10(8):R83. doi: 10.1186/gb-2009-10-8-r83. Epub 2009 Aug 14.

7.

BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing.

Kao WC, Stevens K, Song YS.

Genome Res. 2009 Oct;19(10):1884-95. doi: 10.1101/gr.095299.109. Epub 2009 Aug 6.

8.

Swift: primary data analysis for the Illumina Solexa sequencing platform.

Whiteford N, Skelly T, Curtis C, Ritchie ME, Löhr A, Zaranek AW, Abnizova I, Brown C.

Bioinformatics. 2009 Sep 1;25(17):2194-9. doi: 10.1093/bioinformatics/btp383. Epub 2009 Jun 23.

9.

SHREC: a short-read error correction method.

Schröder J, Schröder H, Puglisi SJ, Sinha R, Schmidt B.

Bioinformatics. 2009 Sep 1;25(17):2157-63. doi: 10.1093/bioinformatics/btp379. Epub 2009 Jun 19.

PMID:
19542152
10.

De novo transcriptome assembly with ABySS.

Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJ.

Bioinformatics. 2009 Nov 1;25(21):2872-7. doi: 10.1093/bioinformatics/btp367. Epub 2009 Jun 15.

PMID:
19528083
11.

Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing.

Qu W, Hashimoto S, Morishita S.

Genome Res. 2009 Jul;19(7):1309-15. doi: 10.1101/gr.089151.108. Epub 2009 May 13.

12.

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL.

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.

13.

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.

14.

Finding optimal threshold for correction error reads in DNA assembling.

Chin FY, Leung HC, Li WL, Yiu SM.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S15. doi: 10.1186/1471-2105-10-S1-S15.

15.

The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast.

Gresham D, Desai MM, Tucker CM, Jenq HT, Pai DA, Ward A, DeSevo CG, Botstein D, Dunham MJ.

PLoS Genet. 2008 Dec;4(12):e1000303. doi: 10.1371/journal.pgen.1000303. Epub 2008 Dec 12.

16.

De novo fragment assembly with short mate-paired reads: Does the read length matter?

Chaisson MJ, Brinza D, Pevzner PA.

Genome Res. 2009 Feb;19(2):336-46. doi: 10.1101/gr.079053.108. Epub 2008 Dec 3.

17.

Population genetic inference from resequencing data.

Jiang R, Tavaré S, Marjoram P.

Genetics. 2009 Jan;181(1):187-97. doi: 10.1534/genetics.107.080630. Epub 2008 Nov 3. Erratum in: Genetics. 2012 Feb;190(2):829-30.

18.

Probabilistic base calling of Solexa sequencing data.

Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F.

BMC Bioinformatics. 2008 Oct 13;9:431. doi: 10.1186/1471-2105-9-431.

19.

Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Li H, Ruan J, Durbin R.

Genome Res. 2008 Nov;18(11):1851-8. doi: 10.1101/gr.078212.108. Epub 2008 Aug 19.

20.

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.

Erlich Y, Mitra PP, delaBastide M, McCombie WR, Hannon GJ.

Nat Methods. 2008 Aug;5(8):679-82. doi: 10.1038/nmeth.1230. Epub 2008 Jul 6.

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