title: SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.
abstract: BACKGROUND
  The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects.
  
  
  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 genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM.
  
  
  CONCLUSIONS
  Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net .
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Diego C B
authors.initials: DC
authors.lastname: Mariano
authors.affiliation: National Reference Laboratory for Aquatic Animal Diseases of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Felipe L
authors.initials: FL
authors.lastname: Pereira
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Edgar L
authors.initials: EL
authors.lastname: Aguiar
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Letícia C
authors.initials: LC
authors.lastname: Oliveira
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Leandro
authors.initials: L
authors.lastname: Benevides
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Luís C
authors.initials: LC
authors.lastname: Guimarães
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Edson L
authors.initials: EL
authors.lastname: Folador
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Thiago J
authors.initials: TJ
authors.lastname: Sousa
authors.affiliation: Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, PurbaMedinipur, WB-721172, India.|Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA.
authors.forename: Preetam
authors.initials: P
authors.lastname: Ghosh
authors.affiliation: Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, PurbaMedinipur, WB-721172, India.
authors.forename: Debmalya
authors.initials: D
authors.lastname: Barh
authors.affiliation: National Reference Laboratory for Aquatic Animal Diseases of Ministry of Agriculture, Livestock and Food Supply, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Henrique C P
authors.initials: HC
authors.lastname: Figueiredo
authors.affiliation: Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
authors.affiliation: Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Rommel T J
authors.initials: RT
authors.lastname: Ramos
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil. vasco@icb.ufmg.br.|Federal University of Minas Gerais, Institute of Biological Sciences, Antônio Carlos 6627, Pampulha, 30161-970, Belo Horizonte, Minas Gerais, Brazil. vasco@icb.ufmg.br.
authors.forename: Vasco A C
authors.initials: VA
authors.lastname: Azevedo
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D001483:Base Sequence; D002874:Chromosome Mapping; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D017422:Sequence Analysis, DNA; D012984:Software
keywords: Bacterial genome; Bioinformatics; Genome assembly; Genome finishing; Ion Torrent PGM; Web tool