GMcloser

GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.

An accompanied package, GMvalue, is a tool to determine misassembly sites in contigs and scaffolds. Unlike other related tools, GMvalue can define misassembly categories with several options, and can be applied to assemblies of a large size genome. By using the -e option, GMvalue also generates error-free assemblies by splitting or correcting misassembles.