ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs

• DOI: 10.1093/bioinformatics/btaa253
• Publication Date: 2020-04-14T19:14:52Z
• Authors: Lauren Coombe; Vladimir Nikolić; Justin Chu; Inanc Birol; René L Warren
• Keywords: Sequence assembly; Python; Synteny

The ability to generate high-quality genome sequences is cornerstone modern biological research. Even with recent advancements in sequencing technologies, many assemblies are still not achieving reference-grade. Here, we introduce ntJoin, a tool that leverages structural synteny between draft assembly and reference sequence(s) contiguate correct the former respect latter. Instead of alignments, ntJoin uses lightweight mapping approach based on graph data structure generated from ordered minimizer sketches. can be used variety different applications, including improving reference-grade genome, short-read long-read an closely related species. When scaffolding human using or assembly, improves NGA50 length 23- 13-fold, respectively, under 13 m, <11 GB RAM. Compared existing reference-guided scaffolders, generates highly contiguous faster less memory.