ArticleBMC bioinformatics2024
VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs.
Article in BMC bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 26 citations in OpenAlex.
- Article
- Analysis of Genetic Diversity in Speckled Blue Grouper (Animals : an open access journal from MDPI · 2026Article
- Chromosome-level genome and population resequencing reveal genetic diversity, demographic history, and climate risk in the East Asian relict treePlant diversity · 2026Article
- Population genomics reveals population structure, glacial divergence, and intertidal adaptation in the Chinese chiton (Liolophura sinensis).Communications biology · 2026Article
- Genetic diversity analysis and core collection construction of Macadamia spp. from Yunnan using fourfold degenerate SNP sites.BMC plant biology · 2026Article
- Evaluating Fishing Ban Effectiveness Through Spatiotemporal Changes in Genetic Diversity ofEcology and evolution · 2026Article
- A Genomic Method for Combating Wildlife Trafficking: SNP-Based Traceability of Four Endangered Species in China.Animals : an open access journal from MDPI · 2026Article
- Rapid Genomic Adaptation of Drosophila Melanogaster to Wolbachia Elimination.Microbial ecology · 2026Article
- Genetic legacy and recent cross of two ancient lineages underlie the rebound of the world's rarest primate.Science advances · 2026Article
- Genome-Wide Association Study Dissects the Genetic Architecture of Pericarp Traits in Fresh-Eating Maize.Plants (Basel, Switzerland) · 2025Article
- Chromosome-Level Genome Assembly of the Japanese Zacco platypus for Comparative Genomics.Scientific data · 2025Article
- A curated dataset of great ape genome diversity.Scientific data · 2025Article
- A transcription factor gene CaMYB114 associated with black seed coat in chickpea.BMC plant biology · 2025Article
- Article
- Isolation effects and soil properties drive genetic differentiation in Ormosia microphylla populations.Scientific reports · 2025Article
- Integrating Artificial Intelligence in Next-Generation Sequencing: Advances, Challenges, and Future Directions.Current issues in molecular biology · 2025Review
- VCF2Dis: an ultra-fast and efficient tool to calculate pairwise genetic distance and construct population phylogeny from VCF files.GigaScience · 2025Article
- Drug selection based on pan-genomics genetic features ofFrontiers in microbiology · 2025Article
- Exploring the Influence of Date Palm Cultivars on Soil Microbiota.Microbial ecology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
Principal component analysis (PCA) is an important and widely used unsupervised learning method that determines population structure based on genetic variation. Genome sequencing of thousands of individuals usually generate tens of millions of SNPs, making it challenging for PCA analysis and interpretation. Here we present VCF2PCACluster, a simple, fast and memory-efficient tool for Kinship estimation, PCA and clustering analysis, and visualization based on VCF formatted SNPs. We implemented five Kinship estimation methods and three clustering methods for its users to choose from. Moreover, unlike other PCA tools, VCF2PCACluster possesses a clustering function based on PCA result, which enabling users to automatically and clearly know about population structure. We demonstrated the same accuracy but a higher performance of this tool in performing PCA analysis on tens of millions of SNPs compared to another popular PLINK2 software, especially in peak memory usage that is independent of the number of SNPs in VCF2PCACluster.
Indexed as
Identifiers
What Socratic holds
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 Socratic graph.