KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 38605047.
- Also identified by DOI 10.1038/s41467-024-47562-4 and PMC identifier 11009271.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Long reads that cover more variants per read raise opportunities for accurate haplotype construction, whereas the genotype errors of single nucleotide polymorphisms pose great computational challenges for haplotyping tools. Here we introduce KSNP, an efficient haplotype construction tool based on the de Bruijn graph (DBG). KSNP leverages the ability of DBG in handling high-throughput erroneous reads to tackle the challenges. Compared to other notable tools in this field, KSNP achieves at least 5-fold speedup while producing comparable haplotype results. The time required for assembling human haplotypes is reduced to nearly the data-in time.
Medical subject headings
- Algorithms
- Polymorphism, Single Nucleotide