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RÉFÉRENCES Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. 2013. Genome sequences of rare, uncul-tured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31:533-538. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11:R106. Brent MR. 2008. Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat Rev Genet 9:62-73. Caporaso JG, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335-336. Chiang GT, Clapham P, Qi G, Sale K, Coates G. 2011. Imple-menting a genomic data management system using iRODS in the Wellcome Trust Sanger Institute. BMC Bioinformatics 12:361. Chivian D, Dehal PS, Keller K, Arkin AP. 2013. MetaMicrobe-sOnline: phylogenomic analysis of microbial communities. Nucleic Acids Res 41:D648-654. Dillies MA, et al. 2013. A comprehensive evaluation of nor-malization methods for Illumina high-throughput RNA sequen-cing data analysis. Brief Bioinform in press. Edwards RA, Rohwer F. 2005. Viral metagenomics. Nat Rev Microbiol 3:504-510. Glenn TC. 2011. Field guide to next-generation DNA sequen-cers. Mol Ecol Resour 11:759-769. Logares R, Haverkamp TH, Kumar S, Lanzen A, Nederbragt AJ, Quince C, Kauserud H. 2012. Environmental microbiology through the lens of high-throughput DNA sequencing: synop-sis of current platforms and bioinformatics approaches. J Microbiol Methods 91:106-113. Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2012. Meta- Velvet: an extension of Velvet assembler to de novo metage-nome assembly from short sequence reads. Nucleic Acids Res 40: e155. Peyretaillade E, et al. 2012. Annotation of microsporidian ge-nomes using transcriptional signals. Nat Commun 3:1137. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ. 2011. Removing noise from pyrosequenced amplicons. BMC Bioin-formatics 12:38. Roux S, Faubladier M, Mahul A, Paulhe N, Bernard A, Debroas D, Enault F. 2011. Metavir: a web server dedicated to virome analysis. Bioinformatics 27:3074-3075. Soneson C, Delorenzi M. 2013. A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics 14:91. Temperton B, Giovannoni SJ. 2012. Metagenomics: micro-bial diversity through a scratched lens. Curr Opin Microbiol 15:605-612. Wandelt S, Rheinländer A, Bux M, Thalheim L, Haldemann B, Leser U. 2012. Data management challenges in next genera-tion sequencing, Datenbank-Spektrum 12:161-171. Wommack KE, Bhavsar J, Polson SW, Chen J, Dumas M, Srini-vasiah S, Furman M, Jamindar S, Nasko DJ. 2012. VIROME: a standard operating procedure for analysis of viral metage-nome sequences. Stand Genomic Sci 6:427-439. Yarza P, et al. 2013. Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence data-base for all species with validly published names. Syst Appl Microbiol 36:69-73. e-Infrastructures pour la Génomique et la Biologie à Grande Echelle : http://www.france-grilles.fr/IMG/pdf/E-InfraGeno- Bio-rapport_final.pdf. Greengenes : http://greengenes.lbl.gov/ RDP : http://rdp.cme.msu.edu/ SILVA : http://www.arb-silva.de/ PROSPECTIVE DE L’INSTITUT ECOLOGIE ET ENVIRONNEMENT DU CNRS 33 SITES INTERNET


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