ArticleNucleic acids research2021
SpecHap: a diploid phasing algorithm based on spectral graph theory.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Graph-based deep reinforcement learning for haplotype assembly with Ralphi.Genome research · 2025Article
- BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.Nucleic acids research · 2023Article
- SpecHLA enables full-resolution HLA typing from sequencing data.Cell reports methods · 2023Article
- Incorporating cell hierarchy to decipher the functional diversity of single cells.Nucleic acids research · 2023Article
- Interrogating the Human Diplome: Computational Methods, Emerging Applications, and Challenges.Methods in molecular biology (Clifton, N.J.) · 2023Article
- HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences.GigaScience · 2022Article
- Chromosome-Level Haplotype Assembly forFrontiers in genetics · 2022Article
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Authors and funding
4 authors.
Funding
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Abstract
Haplotype phasing plays an important role in understanding the genetic data of diploid eukaryotic organisms. Different sequencing technologies (such as next-generation sequencing or third-generation sequencing) produce various genetic data that require haplotype assembly. Although multiple diploid haplotype phasing algorithms exist, only a few will work equally well across all sequencing technologies. In this work, we propose SpecHap, a novel haplotype assembly tool that leverages spectral graph theory. On both in silico and whole-genome sequencing datasets, SpecHap consumed less memory and required less CPU time, yet achieved comparable accuracy with state-of-art methods across all the test instances, which comprises sequencing data from next-generation sequencing, linked-reads, high-throughput chromosome conformation capture, PacBio single-molecule real-time, and Oxford Nanopore long-reads. Furthermore, SpecHap successfully phased an individual Ambystoma mexicanum, a species with gigantic diploid genomes, within 6 CPU hours and 945MB peak memory usage, while other tools failed to yield results either due to memory overflow (40GB) or time limit exceeded (5 days). Our results demonstrated that SpecHap is scalable, efficient, and accurate for diploid phasing across many sequencing platforms.
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Registered trials
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