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SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Diego C. B. Mariano, Felipe L. Pereira, Edgar L. Aguiar, Letícia C. Oliveira, Leandro Benevides, Luís C. Guimarães, Edson L. Folador, Thiago J. Sousa, Preetam Ghosh, Debmalya Barh, Henrique C. P. Figueiredo, Artur Silva (+2 others)
2016 BMC Bioinformatics  
We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM.  ...  Results: In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial  ...  Acknowledgements This study was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG), Ministério da Agricultura  ... 
doi:10.1186/s12859-016-1344-7 pmid:28105921 pmcid:PMC5249034 fatcat:b3daecnlvren3alcbupdqwtj3m

Genome Sequence of Corynebacterium ulcerans Strain FRC11

Leandro de Jesus Benevides, Marcus Vinicius Canário Viana, Diego César Batista Mariano, Flávia de Souza Rocha, Priscilla Carolinne Bagano, Edson Luiz Folador, Felipe Luiz Pereira, Fernanda Alves Dorella, Carlos Augusto Gomes Leal, Alex Fiorini Carvalho, Siomar de Castro Soares, Adriana Carneiro (+7 others)
2015 Genome Announcements  
Here, we present the genome sequence of Corynebacterium ulcerans strain FRC11.  ...  The genome includes one circular chromosome of 2,442,826 bp (53.35% G؉C content), and 2,210 genes were predicted, 2,146 of which are putative protein-coding genes, with 12 rRNAs and 51 tRNAs; 1 pseudogene  ...  ACKNOWLEDGMENTS This work was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Ministério da Pesca e Aquicultura, and Fundação de Amparo à Pesquisa do Estado de Minas  ... 
doi:10.1128/genomea.00112-15 pmid:25767241 pmcid:PMC4357763 fatcat:pctdqjyvsfetje6gegxvhj6o6e

Novel Computational Techniques For Mapping And Classifying Next-Generation Sequencing Data

Karel Břinda, Gregory Kucherov, Valentina Boeva
2016 Zenodo  
Since their emergence around 2006, Next-Generation Sequencing technologies have been revolutionizing biological and medical research.  ...  We provide Ococo, the first online consensus caller that implements a smart statistics for individual genomic positions using compact bit counters.  ...  General approach The general approach for sequencing is similar for all technologies.  ... 
doi:10.5281/zenodo.1045317 fatcat:agbwpocisncwvihn2ij5q3ongq


2014 Advances in Animal Biosciences  
There is clearly a need for further enhancement of surveillance technologies, as well as better vaccines and antiviral agents to combat these diseases.  ...  Virus serotype is important as the protection generated by BTV vaccines is type-specific.  ...  Conclusion The single-step approach resulted in higher accuracy of genomic breeding values in comparison with BLUP-SNP for a small reference population.  ... 
doi:10.1017/s2040470014000028 fatcat:2x2igc5erngbtejpnvvlwcukoy