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Results: 1 to 20 of 95

1.

All Your Base: a fast and accurate probabilistic approach to base calling.

Massingham T, Goldman N.

Genome Biol. 2012 Feb 29;13(2):R13. doi: 10.1186/gb-2012-13-2-r13.

PMID:
22377270
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
22569177
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.

Ye C, Hsiao C, Corrada Bravo H.

Bioinformatics. 2014 May 1;30(9):1214-9. doi: 10.1093/bioinformatics/btu010. Epub 2014 Jan 9.

PMID:
24413520
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Base calling for high-throughput short-read sequencing: dynamic programming solutions.

Das S, Vikalo H.

BMC Bioinformatics. 2013 Apr 15;14:129. doi: 10.1186/1471-2105-14-129.

PMID:
23586484
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
22253293
[PubMed - indexed for MEDLINE]
Free PMC Article
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
[PubMed - indexed for MEDLINE]
Free Article
7.

Fast mapping of short sequences with mismatches, insertions and deletions using index structures.

Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J.

PLoS Comput Biol. 2009 Sep;5(9):e1000502. doi: 10.1371/journal.pcbi.1000502. Epub 2009 Sep 11.

PMID:
19750212
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Error correction of high-throughput sequencing datasets with non-uniform coverage.

Medvedev P, Scott E, Kakaradov B, Pevzner P.

Bioinformatics. 2011 Jul 1;27(13):i137-41. doi: 10.1093/bioinformatics/btr208.

PMID:
21685062
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.

Boisvert S, Laviolette F, Corbeil J.

J Comput Biol. 2010 Nov;17(11):1519-33. doi: 10.1089/cmb.2009.0238. Epub 2010 Oct 20.

PMID:
20958248
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold.

Menelaou A, Marchini J.

Bioinformatics. 2013 Jan 1;29(1):84-91. doi: 10.1093/bioinformatics/bts632. Epub 2012 Oct 23.

PMID:
23093610
[PubMed - indexed for MEDLINE]
Free Article
11.

SNP calling by sequencing pooled samples.

Raineri E, Ferretti L, Esteve-Codina A, Nevado B, Heath S, Pérez-Enciso M.

BMC Bioinformatics. 2012 Sep 20;13:239. doi: 10.1186/1471-2105-13-239.

PMID:
22992255
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

pIRS: Profile-based Illumina pair-end reads simulator.

Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, Chen Y, Mu D, Zhang H, Li N, Yue Z, Bai F, Li H, Fan W.

Bioinformatics. 2012 Jun 1;28(11):1533-5. doi: 10.1093/bioinformatics/bts187. Epub 2012 Apr 15.

PMID:
22508794
[PubMed - indexed for MEDLINE]
Free Article
13.

naiveBayesCall: an efficient model-based base-calling algorithm for high-throughput sequencing.

Kao WC, Song YS.

J Comput Biol. 2011 Mar;18(3):365-77. doi: 10.1089/cmb.2010.0247.

PMID:
21385040
[PubMed - indexed for MEDLINE]
14.

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects.

Farrer RA, Henk DA, MacLean D, Studholme DJ, Fisher MC.

Sci Rep. 2013;3:1512. doi: 10.1038/srep01512.

PMID:
23518929
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing.

Lou DI, Hussmann JA, McBee RM, Acevedo A, Andino R, Press WH, Sawyer SL.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19872-7. doi: 10.1073/pnas.1319590110. Epub 2013 Nov 15.

PMID:
24243955
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data.

Wirawan A, Harris RS, Liu Y, Schmidt B, Schröder J.

BMC Bioinformatics. 2014 May 6;15:131. doi: 10.1186/1471-2105-15-131.

PMID:
24885381
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Discovering motifs that induce sequencing errors.

Allhoff M, Schönhuth A, Martin M, Costa IG, Rahmann S, Marschall T.

BMC Bioinformatics. 2013;14 Suppl 5:S1. doi: 10.1186/1471-2105-14-S5-S1. Epub 2013 Apr 10.

PMID:
23735080
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.

Zhang J, Wang J, Wu Y.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S6. doi: 10.1186/1471-2105-13-S6-S6.

PMID:
22537045
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
23320938
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

ParticleCall: a particle filter for base calling in next-generation sequencing systems.

Shen X, Vikalo H.

BMC Bioinformatics. 2012 Jul 9;13:160. doi: 10.1186/1471-2105-13-160.

PMID:
22776067
[PubMed - indexed for MEDLINE]
Free PMC Article

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