ArticleBMC genomics2017
Hybrid assembly with long and short reads improves discovery of gene family expansions.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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The trial behind it
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
32 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Hybrid Whole-Genome Sequencing ofInternational journal of molecular sciences · 2026Article
- High-quality chromosome-scale genome assembly and adaptive evolution analysis of Yangtze endemic Coreius guichenoti.Genes & genomics · 2026Article
- Pan-genomics of polyploid crops: from complexity to breeding.Frontiers in plant science · 2026Review
- Evaluating the Assembly Strategy of a Fungal Genome from Metagenomic Data:Journal of fungi (Basel, Switzerland) · 2025Article
- Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification.Viruses · 2025Article
- Trematode Genomics and Proteomics.Advances in experimental medicine and biology · 2024Article
- Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes.Biomolecules · 2023Review
- IntegratedNAR genomics and bioinformatics · 2023Article
- A Germin-Like Protein GLP1 of Legumes Mediates Symbiotic Nodulation by Interacting with an Outer Membrane Protein of Rhizobia.Microbiology spectrum · 2023Article
- Methods to improve the accuracy of next-generation sequencing.Frontiers in bioengineering and biotechnology · 2023Review
- Comprehensive whole genome sequencing with hybrid assembly of multi-drug resistantCurrent research in microbial sciences · 2023Article
- Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions.Scientific reports · 2022Article
- metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies.Genome biology · 2022Article
- On a greedy approach for genome scaffolding.Algorithms for molecular biology : AMB · 2022Article
- Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird.Genetics · 2022Article
- Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors inMicroorganisms · 2021Article
- Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time.International journal of molecular sciences · 2021Review
- instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder.Genome biology · 2020Article
- Opportunities and challenges in long-read sequencing data analysis.Genome biology · 2020Review
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
backgroundLong-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation.
methodsWe developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation.
resultsCompared to two other assembly protocols, Alpaca demonstrated the most reference agreement and repeat capture on the rice genome. On three accessions of the model legume Medicago truncatula, Alpaca generated the most agreement to a conspecific reference and predicted tandemly repeated genes absent from the other assemblies.
conclusionOur results suggest Alpaca is a useful tool for investigating structural and copy number variation within de novo assemblies of sampled populations.
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