title: GapBlaster-A Graphical Gap Filler for Prokaryote Genomes.
abstract: The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer.
authors.affiliation: Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Pablo H C G
authors.initials: PH
authors.lastname: de Sá
authors.affiliation: Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Fábio
authors.initials: F
authors.lastname: Miranda
authors.affiliation: Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Adonney
authors.initials: A
authors.lastname: Veras
authors.affiliation: Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Diego Magalhães
authors.initials: DM
authors.lastname: de Melo
authors.affiliation: Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil.
authors.forename: Siomar
authors.initials: S
authors.lastname: Soares
authors.affiliation: Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Kenny
authors.initials: K
authors.lastname: Pinheiro
authors.affiliation: Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Luis
authors.initials: L
authors.lastname: Guimarães
authors.affiliation: Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Vasco
authors.initials: V
authors.lastname: Azevedo
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
mesh_terms: D066289:Data Curation; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D011387:Prokaryotic Cells / Q000378:metabolism*; D012015:Reference Standards; D012984:Software