ArticleLife science alliance2023
New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads.
Article in Life science alliance, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Reference-Guided Chromosome-Scale Genome Assembly With Insights on Population Genomics of the Atlantic Goliath Grouper (Ecology and evolution · 2026Article
- Genome-based insights into metal co-resistance in Amazonian mercury-resistant bacteria: ecological lifestyle and biosafety implications for bioremediation.Microbiology spectrum · 2026Article
- Development of an Oxford nanopore sequencing technology-based whole genome sequencing method for Plasmodium falciparum to support malaria molecular surveillance.Scientific reports · 2026Article
- Population Genomic Analyses Reveal Geographic Structure in Rhizoctonia solani AG1-IA Isolates Associated With Agronomic Crops.Molecular ecology · 2026Article
- A trio-binning approach for genome assembly reveals extensive structural variation between two Cannabis cultivars: Punto Rojo and Cherry Pie.G3 (Bethesda, Md.) · 2026Article
- Genetic diversity and comparative genomics across Leishmania (Viannia) species.Communications biology · 2025Article
- Current Progress in Phased Genome Assembly from Long-Read DNA Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Unveiling potential virulence determinants inMicrobiology spectrum · 2024Article
- A phased genome assembly of a Colombian Trypanosoma cruzi TcI strain and the evolution of gene families.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Building de novo genome assemblies for complex genomes is possible thanks to long-read DNA sequencing technologies. However, maximizing the quality of assemblies based on long reads is a challenging task that requires the development of specialized data analysis techniques. We present new algorithms for assembling long DNA sequencing reads from haploid and diploid organisms. The assembly algorithm builds an undirected graph with two vertices for each read based on minimizers selected by a hash function derived from the k-mer distribution. Statistics collected during the graph construction are used as features to build layout paths by selecting edges, ranked by a likelihood function. For diploid samples, we integrated a reimplementation of the ReFHap algorithm to perform molecular phasing. We ran the implemented algorithms on PacBio HiFi and Nanopore sequencing data taken from haploid and diploid samples of different species. Our algorithms showed competitive accuracy and computational efficiency, compared with other currently used software. We expect that this new development will be useful for researchers building genome assemblies for different species.
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