ArticleBMC bioinformatics2020
LDkit: a parallel computing toolkit for linkage disequilibrium analysis.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 14 citations in OpenAlex.
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- Selection of genetic instruments in Mendelian randomisation studies of sleep traits.Sleep medicine · 2023Review
- GWLD: an R package for genome-wide linkage disequilibrium analysis.G3 (Bethesda, Md.) · 2023Article
- A global phylogenomic analysis of the shiitake genusProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Genomic basis for drought resistance in European beech forests threatened by climate change.eLife · 2021Article
- Root restriction accelerates genomic target identification in quinoa under controlled conditions.Physiologia plantarumArticle
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLinkage disequilibrium (LD) analysis is broadly utilized in genetics to understand the evolutionary and demographic history and helps geneticists identify genes associated with interested inherited traits, such as diseases. There are some tools for linkage disequilibrium analysis either in a local or online way; however, there has been no such tool supporting both graphical user interface (GUI) and parallel computing.
resultsWe developed a GUI software called LDkit for LD analysis, which supports parallel computing. The LDkit supports both variant call format (VCF) and PLINK 'ped + map' format. At the same time, users could also just analyze a subset of individuals from the whole population. The LDkit reads the data by block and then paralleled the computation process by monitoring the usage of processes. Assessment on the Human 1000 genome data showed that when paralleled with 32 threads, the running time was reduced to less than 6 minutes from ~77 minutes using the chromosome 22 dataset with 1,103,547 SNPs and 2504 individuals.
conclusionsThe software LDkit can be effectively used to calculate and plot LD decay, LD block, and linkage disequilibrium analysis between a site and a given region. Most importantly, both graphical user interface (GUI) and stand-alone packages are available for users' convenience. LDkit was written in JAVA language under cross-platform support.
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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.