ArticlePLoS computational biology2015
ConPADE: genome assembly ploidy estimation from next-generation sequencing data.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 35 citations in OpenAlex.
- CNVeil resolves haplotype-specific copy number and uncovers subclonal architecture hidden from total copy number profiling in single-cell cancer genomes.bioRxiv : the preprint server for biology · 2026Article
- Whole-Genome Sequence of Potamopyrgus antipodarum-A Model System for the Maintenance of Sexual Reproduction-Reveals a Recent Whole-Genome Duplication.Genome biology and evolution · 2025Article
- Diploidization in a wild rice allopolyploid is both episodic and gradual.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genome-wide analysis tracks the emergence of intraspecific polyploids in Phragmites australis.npj biodiversity · 2024Article
- Transcriptome Analysis Reveals Potential Mechanism in Storage Protein Trafficking within Developing Grains of Common Wheat.International journal of molecular sciences · 2022Article
- Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies.GigaScience · 2022Article
- Limited allele-specific gene expression in highly polyploid sugarcane.Genome research · 2022Article
- A tetrasomic inheritance model and likelihood-based method for mapping quantitative trait loci in autotetraploid species.The New phytologist · 2021Article
- Analysis of Aneuploidy Spectrum From Whole-Genome Sequencing Provides Rapid Assessment of Clonal Variation Within Established Cancer Cell Lines.Cancer informatics · 2021Article
- Utilization of Tissue Ploidy Level Variation inG3 (Bethesda, Md.) · 2019Article
- A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens.Frontiers in plant science · 2019Article
- Genetic Mapping With Allele Dosage Information in TetraploidFrontiers in plant science · 2019Article
- Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content.Plant biotechnology journal · 2018Article
- nQuire: a statistical framework for ploidy estimation using next generation sequencing.BMC bioinformatics · 2018Article
- Genome-reconstruction for eukaryotes from complex natural microbial communities.Genome research · 2018Article
- Current Strategies of Polyploid Plant Genome Sequence Assembly.Frontiers in plant science · 2018Review
- The Challenge of Analyzing the Sugarcane Genome.Frontiers in plant science · 2018Review
- GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane.BMC genomics · 2017Article
- Variant calling in polyploids for population and quantitative genetics.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As a result of improvements in genome assembly algorithms and the ever decreasing costs of high-throughput sequencing technologies, new high quality draft genome sequences are published at a striking pace. With well-established methodologies, larger and more complex genomes are being tackled, including polyploid plant genomes. Given the similarity between multiple copies of a basic genome in polyploid individuals, assembly of such data usually results in collapsed contigs that represent a variable number of homoeologous genomic regions. Unfortunately, such collapse is often not ideal, as keeping contigs separate can lead both to improved assembly and also insights about how haplotypes influence phenotype. Here, we describe a first step in avoiding inappropriate collapse during assembly. In particular, we describe ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, we report findings regarding errors in sequencing. The method can be used for whole genome shotgun (WGS) sequencing data. We also show applicability of the method for variant calling and allele dosage estimation. Results for simulated and real datasets are discussed and provide evidence that ConPADE performs well as long as enough sequencing coverage is available, or the true contig ploidy is low. We show that ConPADE may also be used for related applications, such as the identification of duplicated genes in fragmented assemblies, although refinements are needed.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.