An Integrated Approach to Comparative Assembly

We describe a novel approach to comparative assembly that directly integrates anchoring alignments into the contig assembly process, enabling the extension of contig construction through the boundaries of repeat nodes in a compressed de Bruijn graph. Our method exploits anchoring alignments, paired-read constraints and read threading as path selection heuristics while an assembly graph is transversed during contig construction. Tests and benchmarks against preeminent implementations of both comparative and de novo assembly models demonstrate that the approach can significantly increase the contiguity of an assembly without inducing a large number of misjoins and structural errors.