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Items: 1 to 20 of 93

1.

Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies.

Machado M, Magalhães WC, Sene A, Araújo B, Faria-Campos AC, Chanock SJ, Scott L, Oliveira G, Tarazona-Santos E, Rodrigues MR.

Investig Genet. 2011 Feb 1;2(1):3. doi: 10.1186/2041-2223-2-3.

2.
3.

Assembling genomic DNA sequences with PHRAP.

de la Bastide M, McCombie WR.

Curr Protoc Bioinformatics. 2007 Mar;Chapter 11:Unit11.4. doi: 10.1002/0471250953.bi1104s17.

PMID:
18428783
4.
5.

Consed: a graphical tool for sequence finishing.

Gordon D, Abajian C, Green P.

Genome Res. 1998 Mar;8(3):195-202.

6.

Consed: a graphical editor for next-generation sequencing.

Gordon D, Green P.

Bioinformatics. 2013 Nov 15;29(22):2936-7. doi: 10.1093/bioinformatics/btt515. Epub 2013 Aug 31.

7.

Characterizing bias in population genetic inferences from low-coverage sequencing data.

Han E, Sinsheimer JS, Novembre J.

Mol Biol Evol. 2014 Mar;31(3):723-35. doi: 10.1093/molbev/mst229. Epub 2013 Nov 27.

8.

PolyPhred analysis software for mutation detection from fluorescence-based sequence data.

Montgomery KT, Iartchouck O, Li L, Loomis S, Obourn V, Kucherlapati R.

Curr Protoc Hum Genet. 2008 Oct;Chapter 7:Unit 7.16. doi: 10.1002/0471142905.hg0716s59.

PMID:
18972372
9.

Generation of artificial FASTQ files to evaluate the performance of next-generation sequencing pipelines.

Frampton M, Houlston R.

PLoS One. 2012;7(11):e49110. doi: 10.1371/journal.pone.0049110. Epub 2012 Nov 12.

10.

An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.

Wang Y, Lu J, Yu J, Gibbs RA, Yu F.

Genome Res. 2013 May;23(5):833-42. doi: 10.1101/gr.146084.112. Epub 2013 Jan 7.

11.

A graph-based approach for designing extensible pipelines.

Rodrigues MR, Magalhães WC, Machado M, Tarazona-Santos E.

BMC Bioinformatics. 2012 Jul 12;13:163. doi: 10.1186/1471-2105-13-163.

12.

NGSPE: A pipeline for end-to-end analysis of DNA sequencing data and comparison between different platforms.

Huang K, Yellapantula V, Baier L, Dinu V.

Comput Biol Med. 2013 Sep;43(9):1171-6. doi: 10.1016/j.compbiomed.2013.05.025. Epub 2013 Jun 13.

PMID:
23930810
13.

SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.

Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P.

BMC Bioinformatics. 2011 May 5;12:134. doi: 10.1186/1471-2105-12-134.

14.

On the design and analysis of next-generation sequencing genotyping for a cohort with haplotype-informative reads.

Zhi D, Liu N, Zhang K.

Methods. 2015 Jun;79-80:41-6. doi: 10.1016/j.ymeth.2015.01.016. Epub 2015 Jan 30.

15.

POSA: perl objects for DNA sequencing data analysis.

Aerts JA, Jungerius BJ, Groenen MA.

BMC Genomics. 2004 Aug 27;5(1):60.

16.
17.

Comparing variant calling algorithms for target-exon sequencing in a large sample.

Lo Y, Kang HM, Nelson MR, Othman MI, Chissoe SL, Ehm MG, Abecasis GR, Zöllner S.

BMC Bioinformatics. 2015 Mar 7;16:75. doi: 10.1186/s12859-015-0489-0.

18.

Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.

Mascher M, Wu S, Amand PS, Stein N, Poland J.

PLoS One. 2013 Oct 3;8(10):e76925. doi: 10.1371/journal.pone.0076925. eCollection 2013.

19.

Large scale sequencing.

Stein L.

Curr Protoc Bioinformatics. 2003 Aug;Chapter 11:Unit11.1. doi: 10.1002/0471250953.bi1101s02. Review.

PMID:
18428694
20.

ngsTools: methods for population genetics analyses from next-generation sequencing data.

Fumagalli M, Vieira FG, Linderoth T, Nielsen R.

Bioinformatics. 2014 May 15;30(10):1486-7. doi: 10.1093/bioinformatics/btu041. Epub 2014 Jan 23.

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