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Items: 1 to 20 of 53

1.

TileQC: a system for tile-based quality control of Solexa data.

Dolan PC, Denver DR.

BMC Bioinformatics. 2008 May 28;9:250. doi: 10.1186/1471-2105-9-250.

2.

Probabilistic base calling of Solexa sequencing data.

Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F.

BMC Bioinformatics. 2008 Oct 13;9:431. doi: 10.1186/1471-2105-9-431.

3.

Genomic DNA sequencing methods.

Favello A, Hillier L, Wilson RK.

Methods Cell Biol. 1995;48:551-69. Review.

PMID:
8531742
4.

ART: a next-generation sequencing read simulator.

Huang W, Li L, Myers JR, Marth GT.

Bioinformatics. 2012 Feb 15;28(4):593-4. doi: 10.1093/bioinformatics/btr708. Epub 2011 Dec 23.

5.

TagDust--a program to eliminate artifacts from next generation sequencing data.

Lassmann T, Hayashizaki Y, Daub CO.

Bioinformatics. 2009 Nov 1;25(21):2839-40. doi: 10.1093/bioinformatics/btp527. Epub 2009 Sep 7.

6.

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.

7.

R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data.

Klein HU, Bartenhagen C, Kohlmann A, Grossmann V, Ruckert C, Haferlach T, Dugas M.

Bioinformatics. 2011 Apr 15;27(8):1162-3. doi: 10.1093/bioinformatics/btr102. Epub 2011 Feb 23.

PMID:
21349869
8.

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
9.

BING: biomedical informatics pipeline for Next Generation Sequencing.

Kriseman J, Busick C, Szelinger S, Dinu V.

J Biomed Inform. 2010 Jun;43(3):428-34. doi: 10.1016/j.jbi.2009.11.003. Epub 2009 Nov 28.

10.

NGSQC: cross-platform quality analysis pipeline for deep sequencing data.

Dai M, Thompson RC, Maher C, Contreras-Galindo R, Kaplan MH, Markovitz DM, Omenn G, Meng F.

BMC Genomics. 2010 Dec 2;11 Suppl 4:S7. doi: 10.1186/1471-2164-11-S4-S7.

11.

Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.

Shin H, Hirst M, Bainbridge MN, Magrini V, Mardis E, Moerman DG, Marra MA, Baillie DL, Jones SJ.

BMC Biol. 2008 Jul 8;6:30. doi: 10.1186/1741-7007-6-30.

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
13.

An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets.

Hosseini P, Tremblay A, Matthews BF, Alkharouf NW.

BMC Res Notes. 2010 Jul 2;3:183. doi: 10.1186/1756-0500-3-183.

14.

Quality scores and SNP detection in sequencing-by-synthesis systems.

Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB.

Genome Res. 2008 May;18(5):763-70. doi: 10.1101/gr.070227.107. Epub 2008 Jan 22.

15.

Sequencing and genome assembly using next-generation technologies.

Nagarajan N, Pop M.

Methods Mol Biol. 2010;673:1-17. doi: 10.1007/978-1-60761-842-3_1. Review.

PMID:
20835789
16.

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
17.

PIQA: pipeline for Illumina G1 genome analyzer data quality assessment.

Martínez-Alcántara A, Ballesteros E, Feng C, Rojas M, Koshinsky H, Fofanov VY, Havlak P, Fofanov Y.

Bioinformatics. 2009 Sep 15;25(18):2438-9. doi: 10.1093/bioinformatics/btp429. Epub 2009 Jul 14.

18.

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.

Dohm JC, Lottaz C, Borodina T, Himmelbauer H.

Nucleic Acids Res. 2008 Sep;36(16):e105. doi: 10.1093/nar/gkn425. Epub 2008 Jul 26.

19.

Swift: primary data analysis for the Illumina Solexa sequencing platform.

Whiteford N, Skelly T, Curtis C, Ritchie ME, Löhr A, Zaranek AW, Abnizova I, Brown C.

Bioinformatics. 2009 Sep 1;25(17):2194-9. doi: 10.1093/bioinformatics/btp383. Epub 2009 Jun 23.

20.

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.

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