Wengan is a new genome assembler that unlike most of the current long-reads assemblers avoids entirely the all-vs-all read comparison. The key idea behind Wengan is that long-read alignments can be inferred by inferring paths in a sequence graph. To achieve this, Wengan builds a new sequence graph called the Synthetic Scaffolding Graph. The SSG is built from a spectrum of synthetic mate-pair libraries extracted from raw long-reads. Longer alignments are then obtained by performing a transitive reduction of the edges. Another distinct feature of Wengan is that it performs self-validation by following the read information. Wengan identifies miss-assemblies at different steps of the assembly process. For more information about the algorithmic ideas behind Wengan, please read the preprint available in bioRxiv. The software itself is available here.
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