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bioRxiv · 10.1101/2020.01.13.905240

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

Coombe, L.·Nikolic, V.·Chu, J.·Birol, I.·Warren, R. L.
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Abstract

SummaryThe 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 less than 11 GB of RAM. Compared to existing reference-guided assemblers, ntJoin generates highly contiguous assemblies faster and using less memory. Availability and implementationntJoin is written in C++ and Python, and is freely available at https://github.com/bcgsc/ntjoin. Contactlcoombe@bcgsc.ca

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Coombe, L., Nikolic, V., Chu, J., Birol, I., Warren, R. L.. 2020-01-14. ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs. https://doi.org/10.1101/2020.01.13.905240

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