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GapBlaster specifications

Information


Unique identifier OMICS_12018
Name GapBlaster
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 1.1.1
Stability Stable
Requirements
JDK, Blast or Mummer
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Rommel T. J. Ramos

Publication for GapBlaster

GapBlaster citations

 (5)
library_books

Draft Genome Sequences of Mycobacterium kansasii Clinical Strains

2017
Genome Announc
PMCID: 5454194
PMID: 28572311
DOI: 10.1128/genomeA.00406-17

[…] to improve assembly contiguity, the obtained sets of contigs were integrated using cisa version 1.3 (). the scaffolding process was performed by contiguator (), while gap closing was done with gapblaster version 1.1.1 (). annotation was carried out automatically using the ncbi prokaryotic genome annotation pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok). the total lengths […]

library_books

Draft Genome Sequence of Corynebacterium pseudotuberculosis Strain PA05 Isolated from an Ovine Host in Pará State, Brazil

2017
Genome Announc
PMCID: 5374232
PMID: 28360158
DOI: 10.1128/genomeA.00082-17

[…] the scaffold was generated using mauve version 2.4.0 () with c. pseudotuberculosis strain 1002b (cp012837.1) as the reference genome. gap closure was done using gapblaster () and clc genomics workbench (http://www.clcbio.com). the final scaffolding with six contigs was submitted to the rast (rapid annotations using subsystems technology) server […]

library_books

Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection

2017
Stand Genomic Sci
PMCID: 5282893
PMID: 28163825
DOI: 10.1186/s40793-017-0234-6

[…] pro tool in the lasergene software package (dnastar). the few remaining gaps after redundancy removal were manually closed using local blast or a program developed by our research group called gapblaster [], which uses a reference genome to assemble similar sequences to close the gap using the sequencing reads. for this analysis, we used c. pseudotuberculosis biovar equi strain 316 […]

library_books

Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics

2017
PLoS One
PMCID: 5268413
PMID: 28125655
DOI: 10.1371/journal.pone.0170676

[…] [] software and the redundancies of the contigs were removed with the seqman pro tool of the lasergene software (dnastar). most of the remaining gaps were manually closed using local blastn or using gapblaster software, which uses a reference genome to map sequenced reads to generate sequences that closed the gap. the complete genome of c. pseudotuberculosis 316 was used as a reference., […]

library_books

Approaches for in silico finishing of microbial genome sequences

2017
Genet Mol Biol
PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] and sealer (), utilizes the information of single-end/paired-end reads to extend, and sometimes locally-reassemble, the contigs and close the gaps. another approach, which is employed by fgap () and gapblaster (), uses an auxiliary set of contigs to find sequences that may fill the region based on local alignment. finally, hybrid approaches, such as gmcloser (), may use a combination […]


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GapBlaster institution(s)
Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil; Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil; Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
GapBlaster funding source(s)
Biologia Computacional Coordenação de Aperfeiçoamento de Pessoal de Nível Superior N° 051/ 2013; Conselho Nacional de Desenvolvimento Científico e Tecnológico grant #482799/2013-7

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