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Items: 1 to 20 of 50

1.

freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers.

Renaud G, Kircher M, Stenzel U, Kelso J.

Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.

2.

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.

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.

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach.

Renaud G, Stenzel U, Maricic T, Wiebe V, Kelso J.

Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.

5.

A support vector machine for identification of single-nucleotide polymorphisms from next-generation sequencing data.

O'Fallon BD, Wooderchak-Donahue W, Crockett DK.

Bioinformatics. 2013 Jun 1;29(11):1361-6. doi: 10.1093/bioinformatics/btt172. Epub 2013 Apr 24.

PMID:
23620357
6.

Optimal spliced alignments of short sequence reads.

De Bona F, Ossowski S, Schneeberger K, Rätsch G.

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

PMID:
18689821
7.

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data.

Liu Y, Schröder J, Schmidt B.

Bioinformatics. 2013 Feb 1;29(3):308-15. doi: 10.1093/bioinformatics/bts690. Epub 2012 Nov 29.

PMID:
23202746
8.

Adjust quality scores from alignment and improve sequencing accuracy.

Li M, Nordborg M, Li LM.

Nucleic Acids Res. 2004 Sep 30;32(17):5183-91. Print 2004.

9.

ConDeTri--a content dependent read trimmer for Illumina data.

Smeds L, Künstner A.

PLoS One. 2011;6(10):e26314. doi: 10.1371/journal.pone.0026314. Epub 2011 Oct 19.

10.

Basecalling with LifeTrace.

Walther D, Bartha G, Morris M.

Genome Res. 2001 May;11(5):875-88.

11.

Novel software package for cross-platform transcriptome analysis (CPTRA).

Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN Jr, Yuan JS.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S16. doi: 10.1186/1471-2105-10-S11-S16.

12.

leeHom: adaptor trimming and merging for Illumina sequencing reads.

Renaud G, Stenzel U, Kelso J.

Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.

13.

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
14.

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing.

Bock C, Reither S, Mikeska T, Paulsen M, Walter J, Lengauer T.

Bioinformatics. 2005 Nov 1;21(21):4067-8. Epub 2005 Sep 1.

PMID:
16141249
15.

Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine.

Thomas N, Heather J, Ndifon W, Shawe-Taylor J, Chain B.

Bioinformatics. 2013 Mar 1;29(5):542-50. doi: 10.1093/bioinformatics/btt004. Epub 2013 Jan 9.

PMID:
23303508
16.

GemSIM: general, error-model based simulator of next-generation sequencing data.

McElroy KE, Luciani F, Thomas T.

BMC Genomics. 2012 Feb 15;13:74. doi: 10.1186/1471-2164-13-74.

17.

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data.

Cox MP, Peterson DA, Biggs PJ.

BMC Bioinformatics. 2010 Sep 27;11:485. doi: 10.1186/1471-2105-11-485.

18.

HTQC: a fast quality control toolkit for Illumina sequencing data.

Yang X, Liu D, Liu F, Wu J, Zou J, Xiao X, Zhao F, Zhu B.

BMC Bioinformatics. 2013 Jan 31;14:33. doi: 10.1186/1471-2105-14-33.

19.

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, Goodwin L, Woyke T, Lapidus A, Klenk HP, Cottingham RW, Kyrpides NC.

PLoS One. 2012;7(12):e48837. doi: 10.1371/journal.pone.0048837. Epub 2012 Dec 12.

20.

pyGenClean: efficient tool for genetic data clean up before association testing.

Lemieux Perreault LP, Provost S, Legault MA, Barhdadi A, Dubé MP.

Bioinformatics. 2013 Jul 1;29(13):1704-5. doi: 10.1093/bioinformatics/btt261. Epub 2013 May 6.

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