Approximate $k$-Mer Matching Using Fuzzy Hash Maps

John Healy, Desmond Chambers
2014 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
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
more » ... tations 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.
doi:10.1109/tcbb.2014.2309609 pmid:26355523 fatcat:bbzw4xdig5ccvb55icjqtfwrxy