KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost.
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ABSTRACT:
SUBMITTER: Zhou Q
PROVIDER: S-EPMC11009271 | biostudies-literature | 2024 Apr
REPOSITORIES: biostudies-literature
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KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost.
Zhou Qian Q Ji Fahu F Lin Dongxiao D Liu Xianming X Zhu Zexuan Z Ruan Jue J
Nature communications 20240411 1
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 ...[more]
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