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

Abstract

<jats:title>Abstract</jats:title><jats:sec><jats:title>Summary</jats:title><jats:p>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 less than 11 GB of RAM. Compared to existing reference-guided assemblers, ntJoin generates highly contiguous assemblies faster and using less memory.</jats:p></jats:sec><jats:sec><jats:title>Availability and implementation</jats:title><jats:p>ntJoin is written in C++ and Python, and is freely available at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/bcgsc/ntjoin">https://github.com/bcgsc/ntjoin</jats:ext-link>.</jats:p></jats:sec><jats:sec><jats:title>Contact</jats:title><jats:p><jats:email>lcoombe@bcgsc.ca</jats:email></jats:p></jats:sec>