Graphical contig analyzer for all sequencing platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes

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Title	Graphical contig analyzer for all sequencing platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes
Authors	Rommel Thiago Jucá Ramos¹, Adriana R Carneiro¹, Pablo H Caracciolo¹, Vasco Azevedo², Maria Paula C Schneider¹, Debmalya Barh³*& Artur Silva¹
Affiliation	¹Instituto de Cięncias Biológicas, Universidade Federal do Pará, Belém, PA, Brazil; ²Instituto de Cięncias Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; ³Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal-721172, India.
Email	dr.barh@gmail.com; *Corresponding author
Article Type	Software
Date	Received May 20, 2013; Accepted May 27, 2013; Published June 29, 2013
Abstract	Genome assembly has always been complicated due to the inherent difficulties of sequencing technologies, as well the computational methods used to process sequences. Although many of the problems for the generation of contigs from reads are well known, especially those involving short reads, the orientation and ordination of contigs in the finishing stages is still very challenging and time consuming, as it requires the manual curation of the contigs to guarantee correct identification them and prevent misassembly. Due to the large numbers of sequences that are produced, especially from the reads produced by next generation sequencers, this process demands considerable manual effort, and there are few software options available to facilitate the process. To address this problem, we have developed the Graphic Contig Analyzer for All Sequencing Platforms (G4ALL): a stand-alone multi-user tool that facilitates the editing of the contigs produced in the assembly process. Besides providing information on the gene products contained in each contig, obtained through a search of the available biological databases, G4ALL produces a scaffold of the genome, based on the overlap of the contigs after curation.
Availability	http://www.genoma.ufpa.br/rramos/softwares/g4all.xhtml
Keywords	Genome assembly, Bioinformatic tools, sequence analysis, software.
Citation	Ramos et al. Bioinformation 9(11): 599-604 (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.