Journal
BIOINFORMATICS
Volume 36, Issue 12, Pages 3885-3887Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btaa253
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Funding
- Genome BC [243FOR, 281ANV]
- Genome Canada [243FOR, 281ANV]
- National Institutes of Health [2R01HG007182-04A1]
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aSummary: The ability to generate high-quality genome sequences is cornerstone to modern biological research. Even with recent advancements in sequencing technologies, many genome assemblies are still not achieving reference-grade. Here, we introduce ntJoin, a tool that leverages structural synteny between a draft assembly and reference sequence(s) to contiguate and correct the former with respect to the latter. Instead of alignments, ntJoin uses a lightweight mapping approach based on a graph data structure generated from ordered minimizer sketches. The tool can be used in a variety of different applications, including improving a draft assembly with a reference grade genome, a short-read assembly with a draft long-read assembly and a draft assembly with an assembly from a closely related species. When scaffolding a human short-read assembly using the reference human genome or a long-read assembly, ntJoin improves the NGA50 length 23- and 13-fold, respectively, in under 13 m, using <11 GB of RAM. Compared to existing reference-guided scaffolders, ntJoin generates highly contiguous assemblies faster and using less memory.
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