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.

TGS-GapCloser: fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads

“…In this work, we chose PBJelly and FGAP software in the gap closure analysis and applied to the Chr19 Mercedes+SLR-superscaffolder assembly with ONT dataset to compare gap filling performance. Other subsequent tools did not display obvious improvements in efficiency and accuracy of gap filling [27]. The evaluation of outputs showed that the gap-closing efficiency of TGS-GapCloser was considerably higher than that of other tools, leaving only 322 gaps compared to 1,730 for PBJelly default, 1,016 gaps for FGAP default and 782 for FGAP with overlap option on ( Table 2), thus enhancing the contig NG50 and NGA50 from 11.4kb to 165.2kb and 9.3kb to 117.6kb, respectively, 3.4-6.1-fold than PBJelly and FGAP.…”

“…The number of gaps could also be efficiently reduced by FGAP [22], which aligned long reads to the gaps using BLAST algorithm [23]. More tools modified the algorithm and extended for different purposes [24][25][26][27][28]. However, most tools mentioned above share the same crucial shortcoming: they only accept pre-error-corrected long reads or alternative assembled contigs.…”

“…The contig N50 was also enhanced from 57.1kb to 364.8kb. Note that most tools have been only used for several bacterial and fungal genomes or small eukaryotes (<1Gb) previously [22,25,27], and it is doubt that it could be applied to this ultra large genome using reasonable computing resources.…”

Gap Filling for a Human MHC Haplotype Sequence

“…There have been a few tools available for gap filling of genome assembly like GapBlaster [8], FGAP [9], G4ALL [10], GapFiller [11] and GapCloser [12]. They use two approaches to fill gaps: paired end reads and assembled contigs from different software.…”

“…They use two approaches to fill gaps: paired end reads and assembled contigs from different software. GapBlaster aligns contigs obtained in the assembly of the genome to a draft of the genome, using BLAST or Mummer, and 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 [8]. FGAP also aligns multiple contigs against a draft genome assembly to find sequences that overlap gaps [9].…”