ArticleGigaScience2017
CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations.
Article in GigaScience, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed, 160 citations in OpenAlex.
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- Host genetic architecture and gut microbiota cooperatively regulate early growth in goats.Animal microbiome · 2026Article
- Whole-genome resequencing suggests adaptive role of copy number variation regions in Indian cattle.Tropical animal health and production · 2026Article
- Identification of the Genetic Characteristics of Copy Number Variation Regions in Diverse Goat Populations.Genes · 2026Article
- Multi-omics dissection of heat stress reveals CIITA as a central regulator of metabolic thermotolerance in cattle (Bos taurus).Communications biology · 2026Article
- Insights into lentil diversity, domestication, and the genetic basis of important agronomic traits through resequencing of 238 Lens accessions.The Plant journal : for cell and molecular biology · 2026Article
- Integrative multi-omics analysis identifies C-type lectin CNVs as functional targets for breeding mastitis-resistant dairy goats.Animal microbiome · 2026Article
- Population structure of wild and cultivated grapevines in Armenia.BMC plant biology · 2026Article
- Genome-wide characterization of copy number variants and their functional relevance in indigenous draught cattle of South Asia.PloS one · 2026Article
- Genomic characterization of host gene alterations in Theileria annulata-transformed leukocytes.Communications biology · 2025Article
- Genetic variation among progeny shapes symbiosis in a basidiomycete with poplar.The New phytologist · 2025Article
- The Genomic Basis of the Svalbard Reindeer's Adaptation to an Extreme Arctic Environment.Genome biology and evolution · 2025Article
- Genetic diversity and reproductive trait selection signal analysis of Bohuai goats based on whole genome sequencing.BMC genomics · 2025Article
- The CNV map construction and ROH analysis of Pinan cattle.BMC genomics · 2025Article
- Article
- A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.Plants (Basel, Switzerland) · 2025Review
- Whole-Genome Sequencing Unveils the Uniqueness of Yushu Yaks (International journal of molecular sciences · 2025Article
- Independent origins and non-parallel selection signatures of triclabendazole resistance in Fasciola hepatica.Nature communications · 2025Article
- SVLearn: a dual-reference machine learning approach enables accurate cross-species genotyping of structural variants.Nature communications · 2025Article
- A comprehensive map of DNA-segment copy number variation in 491 genomes of common wheat uncovers genes associated with multiple agronomic traits.Plant communications · 2025Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background: The increasing amount of sequencing data available for a wide variety of species can be theoretically used for detecting copy number variations (CNVs) at the population level. However, the growing sample sizes and the divergent complexity of nonhuman genomes challenge the efficiency and robustness of current human-oriented CNV detection methods. Results: Here, we present CNVcaller, a read-depth method for discovering CNVs in population sequencing data. The computational speed of CNVcaller was 1-2 orders of magnitude faster than CNVnator and Genome STRiP for complex genomes with thousands of unmapped scaffolds. CNV detection of 232 goats required only 1.4 days on a single compute node. Additionally, the Mendelian consistency of sheep trios indicated that CNVcaller mitigated the influence of high proportions of gaps and misassembled duplications in the nonhuman reference genome assembly. Furthermore, multiple evaluations using real sheep and human data indicated that CNVcaller achieved the best accuracy and sensitivity for detecting duplications. Conclusions: The fast generalized detection algorithms included in CNVcaller overcome prior computational barriers for detecting CNVs in large-scale sequencing data with complex genomic structures. Therefore, CNVcaller promotes population genetic analyses of functional CNVs in more species.
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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.