ArticleGenome research2012
HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed.
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- Parallel evolution of amphioxus and vertebrate small-scale gene duplications.Genome biology · 2022Article
- Assembly of complete diploid-phased chromosomes from draft genome sequences.G3 (Bethesda, Md.) · 2022Article
- Recombination landscape dimorphism and sex chromosome evolution in the dioecious plantPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Strategies of tolerance reflected in two North American maple genomes.The Plant journal : for cell and molecular biology · 2022Article
- Genomic and Experimental Investigations ofJournal of fungi (Basel, Switzerland) · 2021Article
- Conservative route to genome compaction in a miniature annelid.Nature ecology & evolution · 2021Article
- White pupae phenotype of tephritids is caused by parallel mutations of a MFS transporter.Nature communications · 2021Article
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- High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite.PLoS neglected tropical diseases · 2020Article
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- Draft genomes of two outcrossing wild rice,Plant direct · 2020Article
- Deeply conserved synteny resolves early events in vertebrate evolution.Nature ecology & evolution · 2020Article
- Draft Genome Sequence ofMicrobiology resource announcements · 2020Article
13 more citing papers are in PubMed but not listed here.
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10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome shotgun assembly has been a long-standing issue for highly polymorphic genomes, and the advent of next-generation sequencing technologies has made the issue more challenging than ever. Here we present an automated pipeline, HaploMerger, for reconstructing allelic relationships in a diploid assembly. HaploMerger combines a LASTZ-ChainNet alignment approach with a novel graph-based structure, which helps to untangle allelic relationships between two haplotypes and guides the subsequent creation of reference haploid assemblies. The pipeline provides flexible parameters and schemes to improve the contiguity, continuity, and completeness of the reference assemblies. We show that HaploMerger produces efficient and accurate results in simulations and has advantages over manual curation when applied to real polymorphic assemblies (e.g., 4%-5% heterozygosity). We also used HaploMerger to analyze the diploid assembly of a single Chinese amphioxus (Branchiostoma belcheri) and compared the resulting haploid assemblies with EST sequences, which revealed that the two haplotypes are not only divergent but also highly complementary to each other. Taken together, we have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies.
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