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CloudMap: a cloud-based pipeline for analysis of mutant genome sequences.

Minevich G, Park DS, Blankenberg D, Poole RJ, Hobert O.

Genetics. 2012 Dec;192(4):1249-69. doi: 10.1534/genetics.112.144204. Epub 2012 Oct 10.


C. elegans mutant identification with a one-step whole-genome-sequencing and SNP mapping strategy.

Doitsidou M, Poole RJ, Sarin S, Bigelow H, Hobert O.

PLoS One. 2010 Nov 8;5(11):e15435. doi: 10.1371/journal.pone.0015435.


MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq.

Hill JT, Demarest BL, Bisgrove BW, Gorsi B, Su YC, Yost HJ.

Genome Res. 2013 Apr;23(4):687-97. doi: 10.1101/gr.146936.112. Epub 2013 Jan 8.


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.


Identification of mutations in zebrafish using next-generation sequencing.

Henke K, Bowen ME, Harris MP.

Curr Protoc Mol Biol. 2013 Oct 11;104:Unit 7.13. doi: 10.1002/0471142727.mb0713s104.


Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing.

Zhao S, Prenger K, Smith L, Messina T, Fan H, Jaeger E, Stephens S.

BMC Genomics. 2013 Jun 27;14:425. doi: 10.1186/1471-2164-14-425.


Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score.

Lee H, Schatz MC.

Bioinformatics. 2012 Aug 15;28(16):2097-105. doi: 10.1093/bioinformatics/bts330. Epub 2012 Jun 4.


Analysis of multiple ethyl methanesulfonate-mutagenized Caenorhabditis elegans strains by whole-genome sequencing.

Sarin S, Bertrand V, Bigelow H, Boyanov A, Doitsidou M, Poole RJ, Narula S, Hobert O.

Genetics. 2010 Jun;185(2):417-30. doi: 10.1534/genetics.110.116319. Epub 2010 May 3.


Perspectives for identification of mutations in the zebrafish: making use of next-generation sequencing technologies for forward genetic approaches.

Henke K, Bowen ME, Harris MP.

Methods. 2013 Aug 15;62(3):185-96. doi: 10.1016/j.ymeth.2013.05.015. Epub 2013 Jun 5. Review.


RNA-seq-based mapping and candidate identification of mutations from forward genetic screens.

Miller AC, Obholzer ND, Shah AN, Megason SG, Moens CB.

Genome Res. 2013 Apr;23(4):679-86. doi: 10.1101/gr.147322.112. Epub 2013 Jan 8.


Whole genome sequencing and the transformation of C. elegans forward genetics.

Hu PJ.

Methods. 2014 Aug 1;68(3):437-40. doi: 10.1016/j.ymeth.2014.05.008. Epub 2014 May 27.


Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing.

Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I.

PLoS One. 2008;3(12):e4012. doi: 10.1371/journal.pone.0004012. Epub 2008 Dec 24.


Tavaxy: integrating Taverna and Galaxy workflows with cloud computing support.

Abouelhoda M, Issa SA, Ghanem M.

BMC Bioinformatics. 2012 May 4;13:77. doi: 10.1186/1471-2105-13-77.


Next-generation mapping of Arabidopsis genes.

Austin RS, Vidaurre D, Stamatiou G, Breit R, Provart NJ, Bonetta D, Zhang J, Fung P, Gong Y, Wang PW, McCourt P, Guttman DS.

Plant J. 2011 Aug;67(4):715-25. doi: 10.1111/j.1365-313X.2011.04619.x. Epub 2011 Jul 18.


Galaxy CloudMan: delivering cloud compute clusters.

Afgan E, Baker D, Coraor N, Chapman B, Nekrutenko A, Taylor J.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S4. doi: 10.1186/1471-2105-11-S12-S4.


Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms.

You FM, Deal KR, Wang J, Britton MT, Fass JN, Lin D, Dandekar AM, Leslie CA, Aradhya M, Luo MC, Dvorak J.

BMC Genomics. 2012 Jul 31;13:354. doi: 10.1186/1471-2164-13-354.


'PACLIMS': a component LIM system for high-throughput functional genomic analysis.

Donofrio N, Rajagopalon R, Brown D, Diener S, Windham D, Nolin S, Floyd A, Mitchell T, Galadima N, Tucker S, Orbach MJ, Patel G, Farman M, Pampanwar V, Soderlund C, Lee YH, Dean RA.

BMC Bioinformatics. 2005 Apr 12;6:94.


galign: a tool for rapid genome polymorphism discovery.

Shaham S.

PLoS One. 2009 Sep 25;4(9):e7188. doi: 10.1371/journal.pone.0007188.


Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.

Caboche S, Audebert C, Lemoine Y, Hot D.

BMC Genomics. 2014 Apr 5;15:264. doi: 10.1186/1471-2164-15-264.

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