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Items: 1 to 20 of 70

1.

VARiD: a variation detection framework for color-space and letter-space platforms.

Dalca AV, Rumble SM, Levy S, Brudno M.

Bioinformatics. 2010 Jun 15;26(12):i343-9. doi: 10.1093/bioinformatics/btq184.

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.

SHRiMP: accurate mapping of short color-space reads.

Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M.

PLoS Comput Biol. 2009 May;5(5):e1000386. doi: 10.1371/journal.pcbi.1000386. Epub 2009 May 22.

4.

ComB: SNP calling and mapping analysis for color and nucleotide space platforms.

Souaiaia T, Frazier Z, Chen T.

J Comput Biol. 2011 Jun;18(6):795-807. doi: 10.1089/cmb.2011.0027. Epub 2011 May 12.

5.

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.

Bioinformatics. 2010 Mar 15;26(6):730-6. doi: 10.1093/bioinformatics/btq040. Epub 2010 Feb 3.

6.

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
7.

SHRiMP2: sensitive yet practical SHort Read Mapping.

David M, Dzamba M, Lister D, Ilie L, Brudno M.

Bioinformatics. 2011 Apr 1;27(7):1011-2. doi: 10.1093/bioinformatics/btr046. Epub 2011 Jan 28.

PMID:
21278192
8.

HiTEC: accurate error correction in high-throughput sequencing data.

Ilie L, Fazayeli F, Ilie S.

Bioinformatics. 2011 Feb 1;27(3):295-302. doi: 10.1093/bioinformatics/btq653. Epub 2010 Nov 26.

PMID:
21115437
9.

Consensus generation and variant detection by Celera Assembler.

Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, Levy S, Sutton G.

Bioinformatics. 2008 Apr 15;24(8):1035-40. doi: 10.1093/bioinformatics/btn074. Epub 2008 Mar 4.

PMID:
18321888
10.

A probabilistic method for the detection and genotyping of small indels from population-scale sequence data.

Bansal V, Libiger O.

Bioinformatics. 2011 Aug 1;27(15):2047-53. doi: 10.1093/bioinformatics/btr344. Epub 2011 Jun 7.

11.

Optimal spliced alignments of short sequence reads.

De Bona F, Ossowski S, Schneeberger K, R├Ątsch G.

Bioinformatics. 2008 Aug 15;24(16):i174-80. doi: 10.1093/bioinformatics/btn300.

PMID:
18689821
12.

inGAP: an integrated next-generation genome analysis pipeline.

Qi J, Zhao F, Buboltz A, Schuster SC.

Bioinformatics. 2010 Jan 1;26(1):127-9. doi: 10.1093/bioinformatics/btp615. Epub 2009 Oct 30.

13.

A statistical method for the detection of variants from next-generation resequencing of DNA pools.

Bansal V.

Bioinformatics. 2010 Jun 15;26(12):i318-24. doi: 10.1093/bioinformatics/btq214. Erratum in: Bioinformatics. 2016 Oct 15;32(20):3213.

14.

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.

15.

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.

Chen Y, Souaiaia T, Chen T.

Bioinformatics. 2009 Oct 1;25(19):2514-21. doi: 10.1093/bioinformatics/btp486. Epub 2009 Aug 12.

16.

A probabilistic approach for SNP discovery in high-throughput human resequencing data.

Hoberman R, Dias J, Ge B, Harmsen E, Mayhew M, Verlaan DJ, Kwan T, Dewar K, Blanchette M, Pastinen T.

Genome Res. 2009 Sep;19(9):1542-52. doi: 10.1101/gr.092072.109. Epub 2009 Jul 15.

17.

Comparison of sequencing platforms for single nucleotide variant calls in a human sample.

Ratan A, Miller W, Guillory J, Stinson J, Seshagiri S, Schuster SC.

PLoS One. 2013;8(2):e55089. doi: 10.1371/journal.pone.0055089. Epub 2013 Feb 6.

18.

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.

19.

De novo assembly of short sequence reads.

Paszkiewicz K, Studholme DJ.

Brief Bioinform. 2010 Sep;11(5):457-72. doi: 10.1093/bib/bbq020. Epub 2010 Aug 19. Review.

PMID:
20724458
20.

Mixed sequence reader: a program for analyzing DNA sequences with heterozygous base calling.

Chang CT, Tsai CN, Tang CY, Chen CH, Lian JH, Hu CY, Tsai CL, Chao A, Lai CH, Wang TH, Lee YS.

ScientificWorldJournal. 2012;2012:365104. doi: 10.1100/2012/365104. Epub 2012 Jun 18.

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