Among the main challenges that prevent scientists from reaping the benefits of genome assembly
are the high experimental costs, which make it difficult to finish assemblies. Although there
are various computational solutions that assist in the finishing phase, these tools are basically
"black boxes" that do not present enough information about the changes being made in the
genome and often fail to fill in all the gaps left by the assemblers. In this work, these issues
are addressed through the creation of the software GapBlaster, a graphical tool that aims to
reduce the fragmentation of genomes assembly and speed-up finishing the latter. The proposed
algorithm uses as input a FASTA file containing the scaffolds of the genome and one or more
FASTA files containing the contigs, which may come from different assemblers or even from
other sequencing experiments. The contigs are then aligned against the scaffolds through the
software Legacy BLAST, BLAST + or MUMmer and the identified alignments belonging to
the same contig that can also close gaps are then displayed to the user for inspection through
the graphical user interface. GapBlaster’s performance was evaluated on NGS data obtained
from the assemblies of the bacterias Staphylococcus aureus and Rhodobacter sphaeroides,
both acquired from the GAGE project. Additionally, NGS data from the genome assembly of
Corynebacterium pseudotuberculosis was used. Compared with similar tools, the results of
GapBlaster are satisfactory and it has the advantage of offering a graphical user interface for
inspection of closed gaps. GapBlaster was developed in Java and is available for download at
<https://sourceforge.net/projects/gapblaster/>. GapBlaster requires the installation of JDK 8 and
Legacy BLAST, BLAST + or MUMmer.
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