Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph

Paired-end sequencing yields a read from each end of a DNA fragment, typically leaving a gap of unsequenced nucleotides in the middle. Closing this gap using information from other reads in the same sequencing experiment offers the potential to generate longer “pseudo-reads” using short read sequencing platforms. Such long reads may benefit downstream applications such as de novo sequence assembly, gap filling, and variant detection. With these possible applications in mind, we have developed Konnector, a software tool to fill in the nucleotides of the sequence gap between read pairs by navigating a de Bruijn graph. Konnector represents the de Bruijn graph using a Bloom filter, a probabilistic and memory-efficient data structure. Our implementation is able to store the de Bruijn graph using a mean 1.5 bytes of memory per k-mer, which represents a marked improvement over the typical hash table data structure. The memory usage per k-mer is independent of the k-mer length, enabling application of the tool to large genomes. We report the performance of the tool on simulated and experimental datasets, and discuss its utility for downstream analysis. Konnector is open-source software, free for academic use, released under the British Columbia Cancer Agency's academic license. The tool is included with ABySS version 1.5.2 and later, and is available for download from http://www.bcgsc.ca/platform/bioinfo/software/abyss.