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Items: 1 to 20 of 73

1.

Automated correction of genome sequence errors.

Gajer P, Schatz M, Salzberg SL.

Nucleic Acids Res. 2004 Jan 26;32(2):562-9. Print 2004.

2.

Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples.

Hong H, Su Z, Ge W, Shi L, Perkins R, Fang H, Xu J, Chen JJ, Han T, Kaput J, Fuscoe JC, Tong W.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S17. doi: 10.1186/1471-2105-9-S9-S17.

3.

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.

PMID:
21724593
4.

A semi-automated system for analysis and storage of SNPs.

Lehnert V, Holzwarth J, Ott M, Thompson A, Demmak S, Foernzler D.

Hum Mutat. 2001 Apr;17(4):243-54.

PMID:
11295821
5.

Base-calling of automated sequencer traces using phred. I. Accuracy assessment.

Ewing B, Hillier L, Wendl MC, Green P.

Genome Res. 1998 Mar;8(3):175-85.

6.

Using 2k + 2 bubble searches to find single nucleotide polymorphisms in k-mer graphs.

Younsi R, MacLean D.

Bioinformatics. 2015 Mar 1;31(5):642-6. doi: 10.1093/bioinformatics/btu706. Epub 2014 Oct 24.

7.

SNP discovery in non-model organisms using 454 next generation sequencing.

Wheat CW.

Methods Mol Biol. 2012;888:33-53. doi: 10.1007/978-1-61779-870-2_3.

PMID:
22665274
8.

VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering.

Verbist BM, Thys K, Reumers J, Wetzels Y, Van der Borght K, Talloen W, Aerssens J, Clement L, Thas O.

Bioinformatics. 2015 Jan 1;31(1):94-101. doi: 10.1093/bioinformatics/btu587. Epub 2014 Aug 31.

PMID:
25178459
9.

RadixHap: a radix tree-based heuristic for solving the single individual haplotyping problem.

Wang TC, Taheri J, Zomaya AY.

Int J Bioinform Res Appl. 2015;11(1):10-29. doi: 10.1504/IJBRA.2015.067336.

PMID:
25667383
10.

Detection of homologous recombination events in bacterial genomes.

Wang WB, Jiang T, Gardner S.

PLoS One. 2013 Oct 7;8(10):e75230. doi: 10.1371/journal.pone.0075230. eCollection 2013.

11.

Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

Kosugi S, Natsume S, Yoshida K, MacLean D, Cano L, Kamoun S, Terauchi R.

PLoS One. 2013 Oct 8;8(10):e75402. doi: 10.1371/journal.pone.0075402. eCollection 2013. Erratum in: PLoS One. 2014;9(1). doi:10.1371/annotation/cc88d2b5-36e8-441a-ab5f-58a9ed143d6b.

12.

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.

Otto TD, Sanders M, Berriman M, Newbold C.

Bioinformatics. 2010 Jul 15;26(14):1704-7. doi: 10.1093/bioinformatics/btq269. Epub 2010 Jun 18.

13.

Pyrobayes: an improved base caller for SNP discovery in pyrosequences.

Quinlan AR, Stewart DA, Strömberg MP, Marth GT.

Nat Methods. 2008 Feb;5(2):179-81. doi: 10.1038/nmeth.1172. Epub 2008 Jan 13.

PMID:
18193056
14.

SNPsFinder--a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes.

Song J, Xu Y, White S, Miller KW, Wolinsky M.

Bioinformatics. 2005 May 1;21(9):2083-4. Epub 2005 Feb 3.

PMID:
15691853
15.

Automated detection of point mutations using fluorescent sequence trace subtraction.

Bonfield JK, Rada C, Staden R.

Nucleic Acids Res. 1998 Jul 15;26(14):3404-9.

16.

SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip.

Fujisawa H, Horiuchi Y, Harushima Y, Takada T, Eguchi S, Mochizuki T, Sakaguchi T, Shiroishi T, Kurata N.

BMC Bioinformatics. 2009 May 6;10:131. doi: 10.1186/1471-2105-10-131.

17.

RIG: Recalibration and interrelation of genomic sequence data with the GATK.

McCormick RF, Truong SK, Mullet JE.

G3 (Bethesda). 2015 Feb 13;5(4):655-65. doi: 10.1534/g3.115.017012.

18.

Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey.

Kerstens HH, Crooijmans RP, Veenendaal A, Dibbits BW, Chin-A-Woeng TF, den Dunnen JT, Groenen MA.

BMC Genomics. 2009 Oct 16;10:479. doi: 10.1186/1471-2164-10-479.

19.

The complete genome of an individual by massively parallel DNA sequencing.

Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM.

Nature. 2008 Apr 17;452(7189):872-6. doi: 10.1038/nature06884.

PMID:
18421352
20.

Automating sequence-based detection and genotyping of SNPs from diploid samples.

Stephens M, Sloan JS, Robertson PD, Scheet P, Nickerson DA.

Nat Genet. 2006 Mar;38(3):375-81. Epub 2006 Feb 19.

PMID:
16493422

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