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Title

AutoAssemblyD: a graphical user interface system for several genome assemblers

 

Authors

Adonney Allan de Oliveira Veras1, Pablo Henrique Caracciolo Gomes de Sá1, Vasco Azevedo2, Artur Silva1 & Rommel Thiago Jucá Ramos1*

 

Affiliation

1Institute of Biological Sciences, Federal University Pará, Belém, Pará, Brazil; 2Institute of Biological Sciences, Federal University Minas Gerais, Belo Horizonte, Minas Gerais, Brazil

 

Email

rommelthiago@gmail.com; *Corresponding author

 

Article Type

Software

 

Date

Received August 27, 2013; Accepted August 28, 2013; Published September 23, 2013

 

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.

 

Availability

https://sourceforge.net/projects/autoassemblyd

 

Keywords

Next-generation sequencing, Genome Assembly, Bioinformatics.

 

Citation

Veras  et al. Bioinformation 9(16): 840-841 (2013)

 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.