GMcloser

GMcloser closes gaps in genome assemblies by assigning preassembled contigs or long reads (e.g., error-corrected PacBio) to scaffold gaps using alignment-derived likelihood classifiers to improve assembly completeness and accuracy.

Key Features:

• Input types: Accepts preassembled contig sets and long read sets such as error-corrected PacBio reads for gap filling.
• Likelihood-based classifiers: Uses classifiers derived from alignment statistics between scaffolds, contigs, and paired-end reads to assign sequences to gap regions.
• Gap-closing accuracy: Reported to achieve gap-closing accuracy 3–100-fold higher than other available tools.
• Misassembly mitigation: Targets reduction of misassembly errors that have been reported at 20–500-fold higher rates in other gap-closing approaches compared with initial de novo assembly.
• Efficiency: Maintains similar levels of computational efficiency relative to comparable gap-closing tools.
• Auxiliary evaluation (GMvalue): Provides GMvalue to evaluate assembly quality and correct misassemblies excluding single nucleotide polymorphisms (SNPs) and short insertions/deletions.

Scientific Applications:

• Comparative genomics: Improves completeness of genome assemblies used for cross-species genomic comparisons.
• Evolutionary studies: Enhances assembly accuracy for analyses of evolutionary relationships and genomic variation.
• Functional genomics: Increases contiguity and correctness of assemblies for downstream functional annotation and gene analysis.

Methodology:

GMcloser aligns scaffolds, contigs, and paired-end reads, derives alignment statistics to build likelihood-based classifiers, and assigns contigs or long reads (e.g., error-corrected PacBio) to scaffold gaps; GMvalue evaluates assembly quality and corrects misassemblies excluding SNPs and short indels.