Assembling Long Accurate Reads Using de Bruijn Graphs
AbstractAlthough the de Bruijn graphs represent the basis of many genome assemblers, it remains unclear how to construct these graphs for large genomes and large k-mer sizes. This algorithmic challenge has become particularly important with the emergence of long and accurate high-fidelity (HiFi) reads that were recently utilized to generate a semi-manual telomere-to-telomere assembly of the human genome using the alternative string graph assembly approach. To enable fully automated high-quality HiFi assemblies of various genomes, we developed an efficient jumboDB algorithm for constructing the de Bruijn graph for large genomes and large k-mer sizes and the LJA genome assembler that error-corrects HiFi reads and uses jumboDB to construct the de Bruijn graph on the error-corrected reads. Since the de Bruijn graph constructed for a fixed k-mer size is typically either too tangled or too fragmented, LJA uses a new concept of a multiplex de Bruijn graph with varying k-mer sizes. We demonstrate that LJA produces contiguous assemblies of complex repetitive regions in genomes including automated assemblies of various highly-repetitive human centromeres.