gapFinisher

gapFinisher is an automated pipeline to address the crucial yet challenging step of gap filling in de novo genome assembly, particularly in large genomes where unknown sequences or gaps persist in many published genomes across public databases. Despite the availability of various computational tools to solve the gap filling problem, many existing solutions fall short in terms of reliability and correctness of the output.

Leveraging the scaffolding capabilities of SSPACE-LongRead, which utilizes long reads from multiple third-generation sequencing platforms to find links between contigs and combine them, gapFinisher uniquely processes SSPACE-LongRead's output to fill gaps post-scaffolding efficiently. Integrating the controlled use of the previously published gap filling tool FGAP, gapFinisher operates effectively across all standard Linux/UNIX command lines, offering a seamless experience for users.

Through comparative analysis with two other published gap filling tools, PBJelly and GMcloser, gapFinisher demonstrated its ability to fill gaps in draft genomes quickly and reliably, setting it apart from its counterparts. Notably, its serial design allows gapFinisher to scale well from prokaryote genomes to larger ones without increasing the computational footprint, making it a versatile tool for varying-size genome assembly projects.