ArticleBMC bioinformatics2020
Hap10: reconstructing accurate and long polyploid haplotypes using linked reads.
Article in BMC bioinformatics, 2020. 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed, 17 citations in OpenAlex.
- The GIAB genomic stratifications resource for human reference genomes.Nature communications · 2024Article
- When less is more: sketching with minimizers in genomics.Genome biology · 2024Review
- GCphase: an SNP phasing method using a graph partition and error correction algorithm.BMC bioinformatics · 2024Article
- XHap: haplotype assembly using long-distance read correlations learned by transformers.Bioinformatics advances · 2023Article
- Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.Frontiers in genetics · 2023Article
- Article
- Computational methods for chromosome-scale haplotype reconstruction.Genome biology · 2021Review
- Genomics and functional genomics in Leishmania and Trypanosoma cruzi: statuses, challenges and perspectives.Memorias do Instituto Oswaldo Cruz · 2021Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHaplotype information is essential for many genetic and genomic analyses, including genotype-phenotype associations in human, animals and plants. Haplotype assembly is a method for reconstructing haplotypes from DNA sequencing reads. By the advent of new sequencing technologies, new algorithms are needed to ensure long and accurate haplotypes. While a few linked-read haplotype assembly algorithms are available for diploid genomes, to the best of our knowledge, no algorithms have yet been proposed for polyploids specifically exploiting linked reads.
resultsThe first haplotyping algorithm designed for linked reads generated from a polyploid genome is presented, built on a typical short-read haplotyping method, SDhaP. Using the input aligned reads and called variants, the haplotype-relevant information is extracted. Next, reads with the same barcodes are combined to produce molecule-specific fragments. Then, these fragments are clustered into strongly connected components which are then used as input of a haplotype assembly core in order to estimate accurate and long haplotypes.
conclusionsHap10 is a novel algorithm for haplotype assembly of polyploid genomes using linked reads. The performance of the algorithms is evaluated in a number of simulation scenarios and its applicability is demonstrated on a real dataset of sweet potato.
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