title: MapRepeat: an approach for effective assembly of repetitive regions in prokaryotic genomes.
abstract: The newest technologies for DNA sequencing have led to the determination of the primary structure of the genomes of organisms, mainly prokaryotes, with high efficiency and at lower costs. However, the presence of regions with repetitive sequences, in addition to the short reads produced by the Next-Generation Sequencing (NGS) platforms, created a lot of difficulty in reconstructing the original genome in silico. Thus, even today, genome assembly continues to be one of the major challenges in bioinformatics specifically when repetitive sequences are considered. In this paper, we present an approach to assemble repetitive regions in prokaryotic genomes. Our methodology enables (i) the identification of these regions through visual tools, (ii) the characterization of sequences on the extremities of gaps and (iii) the extraction of consensus sequences based on mapping of raw data to a reference genome. We also present a case study on the assembly of regions that encode ribosomal RNAs (rRNA) in the genome of Corynebacterium ulcerans FRC11, in order to show the efficiency of the strategies presented here. The proposed methods and tools will help in finishing genome assemblies, besides reducing the running time and associated costs.
  
  
  BACKGROUND
  All scripts are available at http://github.com/dcbmariano/maprepeat.
authors.affiliation: Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Diego Cb
authors.initials: DC
authors.lastname: Mariano
authors.affiliation: National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Universidade Federal de Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Felipe L
authors.initials: FL
authors.lastname: Pereira
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, Virginia, 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 Fisheries and Aquaculture, Universidade Federal de Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Henrique Cp
authors.initials: HC
authors.lastname: Figueiredo
authors.affiliation: Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa, 01 - Guamá, Belém, PA, Brazil.
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
authors.affiliation: Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa, 01 - Guamá, Belém, PA, Brazil.
authors.forename: Rommel Tj
authors.initials: RT
authors.lastname: Ramos
authors.affiliation: Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Vasco Ac
authors.initials: VA
authors.lastname: Azevedo
keywords: bioinformatics; finishing assemblies; genome assembly; repetitive sequences