ArticleGigaScience2016
AGOUTI: improving genome assembly and annotation using transcriptome data.
Article in GigaScience, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
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- Genome assembly and insights into globally invasive Red-vented Bulbul (Pycnonotus cafer).DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
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- Genome of the most noxious weed water hyacinth (iScience · 2024Article
- High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl.Heliyon · 2023Article
- The Progression in Developing Genomic Resources for Crop Improvement.Life (Basel, Switzerland) · 2023Review
- Genome sequencing ofFrontiers in plant science · 2023Article
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- Genome sequencing and comparative analysis ofiScience · 2022Article
- The Rattlesnake W Chromosome: A GC-Rich Retroelement Refugium with Retained Gene Function Across Ancient Evolutionary Strata.Genome biology and evolution · 2022Article
- Characterization of NRPS and PKS genes involved in the biosynthesis of SMs in Alternaria dauci including the phytotoxic polyketide aldaulactone.Scientific reports · 2022Article
- Structure and evolution of the squamate major histocompatibility complex as revealed by twoFrontiers in genetics · 2022Article
- Genome sequencing of turmeric provides evolutionary insights into its medicinal properties.Communications biology · 2021Article
- Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism.Genome biology and evolution · 2021Article
- Draft genome assembly and annotation of the masked birch caterpillar,Data in brief · 2020Article
- Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel.Genome biology · 2020Article
- Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome.Genome biology and evolution · 2020Article
- The First Draft Genome Assembly of Snow Sheep (Ovis nivicola).Genome biology and evolution · 2020Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenomes sequenced using short-read, next-generation sequencing technologies can have many errors and may be fragmented into thousands of small contigs. These incomplete and fragmented assemblies lead to errors in gene identification, such that single genes spread across multiple contigs are annotated as separate gene models. Such biases can confound inferences about the number and identity of genes within species, as well as gene gain and loss between species.
resultsWe present AGOUTI (Annotated Genome Optimization Using Transcriptome Information), a tool that uses RNA sequencing data to simultaneously combine contigs into scaffolds and fragmented gene models into single models. We show that AGOUTI improves both the contiguity of genome assemblies and the accuracy of gene annotation, providing updated versions of each as output. Running AGOUTI on both simulated and real datasets, we show that it is highly accurate and that it achieves greater accuracy and contiguity when compared with other existing methods.
conclusionAGOUTI is a powerful and effective scaffolder and, unlike most scaffolders, is expected to be more effective in larger genomes because of the commensurate increase in intron length. AGOUTI is able to scaffold thousands of contigs while simultaneously reducing the number of gene models by hundreds or thousands. The software is available free of charge under the MIT license.
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