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Items: 1 to 20 of 666

1.

TotalReCaller: improved accuracy and performance via integrated alignment and base-calling.

Menges F, Narzisi G, Mishra B.

Bioinformatics. 2011 Sep 1;27(17):2330-7. doi: 10.1093/bioinformatics/btr393. Epub 2011 Jun 30.

2.

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

Li H, Durbin R.

Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.

3.

Comparative analysis of algorithms for next-generation sequencing read alignment.

Ruffalo M, LaFramboise T, Koyutürk M.

Bioinformatics. 2011 Oct 15;27(20):2790-6. doi: 10.1093/bioinformatics/btr477. Epub 2011 Aug 19.

4.

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.

5.

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform.

Liu Y, Schmidt B, Maskell DL.

Bioinformatics. 2012 Jul 15;28(14):1830-7. doi: 10.1093/bioinformatics/bts276. Epub 2012 May 9.

6.

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.

7.

Ψ-RA: a parallel sparse index for genomic read alignment.

Oğuzhan Külekci M, Hon WK, Shah R, Scott Vitter J, Xu B.

BMC Genomics. 2011;12 Suppl 2:S7. doi: 10.1186/1471-2164-12-S2-S7. Epub 2011 Jul 27.

8.

SNP calling using genotype model selection on high-throughput sequencing data.

You N, Murillo G, Su X, Zeng X, Xu J, Ning K, Zhang S, Zhu J, Cui X.

Bioinformatics. 2012 Mar 1;28(5):643-50. doi: 10.1093/bioinformatics/bts001. Epub 2012 Jan 16.

9.

BM-BC: a Bayesian method of base calling for Solexa sequence data.

Ji Y, Mitra R, Quintana F, Jara A, Mueller P, Liu P, Lu Y, Liang S.

BMC Bioinformatics. 2012;13 Suppl 13:S6. doi: 10.1186/1471-2105-13-S13-S6. Epub 2012 Aug 24.

10.

BFAST: an alignment tool for large scale genome resequencing.

Homer N, Merriman B, Nelson SF.

PLoS One. 2009 Nov 11;4(11):e7767. doi: 10.1371/journal.pone.0007767.

11.

SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies.

Martin ER, Kinnamon DD, Schmidt MA, Powell EH, Zuchner S, Morris RW.

Bioinformatics. 2010 Nov 15;26(22):2803-10. doi: 10.1093/bioinformatics/btq526. Epub 2010 Sep 21.

12.

Fast and accurate read alignment for resequencing.

Mu JC, Jiang H, Kiani A, Mohiyuddin M, Bani Asadi N, Wong WH.

Bioinformatics. 2012 Sep 15;28(18):2366-73. doi: 10.1093/bioinformatics/bts450. Epub 2012 Jul 18.

13.

BOAT: Basic Oligonucleotide Alignment Tool.

Zhao SQ, Wang J, Zhang L, Li JT, Gu X, Gao G, Wei L.

BMC Genomics. 2009 Dec 3;10 Suppl 3:S2. doi: 10.1186/1471-2164-10-S3-S2.

14.

OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing.

Das S, Vikalo H.

Bioinformatics. 2012 Jul 1;28(13):1677-83. doi: 10.1093/bioinformatics/bts256. Epub 2012 May 7.

15.

Accurate estimation of short read mapping quality for next-generation genome sequencing.

Ruffalo M, Koyutürk M, Ray S, LaFramboise T.

Bioinformatics. 2012 Sep 15;28(18):i349-i355. doi: 10.1093/bioinformatics/bts408.

16.

High quality SNP calling using Illumina data at shallow coverage.

Malhis N, Jones SJ.

Bioinformatics. 2010 Apr 15;26(8):1029-35. doi: 10.1093/bioinformatics/btq092. Epub 2010 Feb 26.

17.

FANSe2: a robust and cost-efficient alignment tool for quantitative next-generation sequencing applications.

Xiao CL, Mai ZB, Lian XL, Zhong JY, Jin JJ, He QY, Zhang G.

PLoS One. 2014 Apr 17;9(4):e94250. doi: 10.1371/journal.pone.0094250. eCollection 2014.

18.

Short read alignment with populations of genomes.

Huang L, Popic V, Batzoglou S.

Bioinformatics. 2013 Jul 1;29(13):i361-70. doi: 10.1093/bioinformatics/btt215.

19.

Long read alignment based on maximal exact match seeds.

Liu Y, Schmidt B.

Bioinformatics. 2012 Sep 15;28(18):i318-i324. doi: 10.1093/bioinformatics/bts414.

20.

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.

Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E.

Bioinformatics. 2013 Sep 15;29(18):2245-52. doi: 10.1093/bioinformatics/btt386. Epub 2013 Jul 3.

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