ArticleBriefings in bioinformatics2023
A practical assembly guideline for genomes with various levels of heterozygosity.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 12 citations in OpenAlex.
- A chromosome-scale genome assembly of Tigridiopalma magnifica.Scientific data · 2026Article
- Identification of genome size and heterozygosity in 510 Jujube (Frontiers in plant science · 2026Article
- The Genome Survey Analysis of Female and MaleGenes · 2025Article
- CloseRead: a tool for assessing assembly errors in immunoglobulin loci applied to vertebrate long-read genome assemblies.Genome biology · 2025Article
- Comparative genomics provides insights into the biogeographic and biochemical diversity of meliaceous species.Nature communications · 2025Article
- The impact of telomere-to-telomere genome assembly in the plant pan-genomics era.Breeding science · 2025Article
- Chromosome-scale assemblies of three Ormosia species: repetitive sequences distribution and structural rearrangement.GigaScience · 2025Article
- Comprehensive analysis of the first complete mitogenome and plastome of a traditional Chinese medicine Viola diffusa.BMC genomics · 2024Article
- A Whole-Genome Survey and the Mitochondrial Genome ofAnimals : an open access journal from MDPI · 2024Article
- Full-length isoform constructor (FLIC) - a tool for isoform discovery based on long reads.Bioinformatics (Oxford, England) · 2022Article
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although current long-read sequencing technologies have a long-read length that facilitates assembly for genome reconstruction, they have high sequence errors. While various assemblers with different perspectives have been developed, no systematic evaluation of assemblers with long reads for diploid genomes with varying heterozygosity has been performed. Here, we evaluated a series of processes, including the estimation of genome characteristics such as genome size and heterozygosity, de novo assembly, polishing, and removal of allelic contigs, using six genomes with various heterozygosity levels. We evaluated five long-read-only assemblers (Canu, Flye, miniasm, NextDenovo and Redbean) and five hybrid assemblers that combine short and long reads (HASLR, MaSuRCA, Platanus-allee, SPAdes and WENGAN) and proposed a concrete guideline for the construction of haplotype representation according to the degree of heterozygosity, followed by polishing and purging haplotigs, using stable and high-performance assemblers: Redbean, Flye and MaSuRCA.
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