Konnector is a scalable de novo assembler for paired-end reads.
It fills in the nucleotides of the sequence gap between read pairs by navigating a de Bruijn graph (DBG) represented by a Bloom filter.
The Bloom filter is a probabilistic and memory-efficient data structure that enables storing the de Bruijn graph using a mean 1.5 bytes of memory per k-mer (our implementation), which represents a marked improvement over the typical hash table data structure employed by most DBG assemblers. The memory usage per k-mer is independent of the k-mer length, enabling application of the tool to large genomes.
The release of Konnector 2.0 introduces the ability to extend paired-end sequences outwards in the de Bruijn graph, in addition to merging reads pairs via connecting paths.
Availability
Konnector is included with ABySS version 1.5.2 and later
Citations
[1] Vandervalk, Benjamin P., Shaun D. Jackman, Anthony Raymond, Hamid Mohamadi, Chen Yang, Dean Attali, James Chu, Rene L. Warren, and Inanc Birol. "Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph." In Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on, pp. 51-58. IEEE, 2014. http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6999126&tag=1
[2] Vandervalk, Benjamin P., Chen Yang, Zhuyi Xue, Karthika Raghavan, Justin Chu, Hamid Mohamadi, Shaun D. Jackman, Readman Chiu, René L. Warren, and Inanç Birol. "Konnector v2. 0: pseudo-long reads from paired-end sequencing data." BMC medical genomics 8, no. Suppl 3 (2015): S1. http://dx.doi.org/10.1186%2F1755-8794-8-S3-S1