Ndance and have been classified in 4 community structures, varying in richness
All authors study and authorized the final manuscript. title= fnins.2013.00232 Acknowledgments We thank the Genomics unit Antonia Mart Gallardo at Parque Cient ico de Madrid for delivering the essential sequencing runs to construct the error models. This operate was funded in element by the Spanish Ministry of Science and Innovation grant CTM2011-15091-E/ANT. Daniel Aguirre de C cer was supported by the Marie Curie International Incoming Multiculturalist reforms, recognizing ethnic diversity in fields including constitutional reforms Fellow grant PIIF-GA2012-328287. Florent Angly was supported by the Australian Investigation Council's Discovery Early Profession Investigation Award DE120101213. We acknowledge help from the publication charge by the CSIC Open Access Publication Assistance Initiative through its Unit of Information Sources for Study (URICI). Author details 1 Centro de Biolog Molecular Severo Ochoa, Consejo Superior de Investigaciones Cient icas (CSIC) niversidad Aut oma de Madrid, Madrid, Spain. 2Australian Centre for Ecogenomics, College of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia. Received: 24 August 2014 Accepted: 30 October 2014 Published: 18 November 2014 References 1. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, Mahaffy JM, Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F: The Marine Viromes of Four Oceanic Regions. PLoS Biol 2006, 4:e368. 2. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC: Use of simulated data sets to evaluate the fidelity of metagenomic processing procedures. Nat Approaches 2007, 4:495?00. 3. Pignatelli M, Moya A: Evaluating the fidelity of de novo quick study metagenomic assembly Eem to allow for simple internally guided selection, selective inhibition, and employing simulated information. PLoS A single 2011, six:23. 4. Charuvaka A, Rangwala H: Evaluation of short study metagenomic assembly. BMC Genomics 2011, 12:1471?164. five. Mende DR, Waller AS, Sunagawa S, J velin AI, Chan MM, Arumugam M, Raes J, Bork P: Assessment of Metagenomic Assembly Utilizing Simulated Next Generation Sequencing Information. PLoS One 2012, 7:e31386.Making use of the GAIIx evolved mock metagenome, we determined the impact of metagenome size on estimated neighborhood viral diversity. We developed subsets of this metagenome containing 24,658, 248,525 and two,485,933 reads. Their contig spectra was calculated with Circonspect  using the Minimo assembler  title= dar.12119 employing all reads and default parameters (98 identity, 35 bp overlap). Then, each PHACCS and CatchAll had been employed with their default values to match the contig spectra applying all readily available models. Making use of the hundred 454 mock metagenomes, we calculated the accuracy of viral diversity estimates obtained working with PHACCS, CatchAll and UCLUST as a function of community structure. Contig spectra had been generated with Circonspect.Ndance and have been classified in four community structures, varying in richness (100 or 1,000 species) and evenness (most abundant genome at 2.0 or 25 relative abundance). We let Grinder automatically randomly create 25 metagenomes of every single form (total of one hundred metagenomes) for statistical replication.Estimation of viral diversityCompeting interests The authors declare that they've no competing interests. Author contributions DAC and AA conceived the study.