title: AutoAssemblyD: a graphical user interface system for several genome assemblers.
abstract: Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates.
  
  
  BACKGROUND
  AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.
authors.affiliation: Institute of Biological Sciences, Federal University Pará, Belém, Pará, Brazil.
authors.forename: Adonney Allan de Oliveira
authors.initials: AA
authors.lastname: Veras
authors.forename: Pablo Henrique Caracciolo Gomes
authors.initials: PH
authors.lastname: de Sá
authors.forename: Vasco
authors.initials: V
authors.lastname: Azevedo
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
authors.forename: Rommel Thiago Jucá
authors.initials: RT
authors.lastname: Ramos
keywords: Bioinformatics; Genome Assembly; Next-generation sequencing