DEploid
Deconvolute Mixed Genomes with Unknown Proportions
Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haplotype searches in a multiple infection setting. This package is primarily developed as part of the Pf3k project, which is a global collaboration using the latest sequencing technologies to provide a high-resolution view of natural variation in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from patient blood sample, which often contains more than one parasite strain, with unknown proportions. This package is used for deconvoluting mixed haplotypes, and reporting the mixture proportions from each sample.
- Version0.5.7
- R versionR (≥ 3.1.0)
- LicenseGPL (≥ 3)
- Needs compilation?Yes
- DEploid citation info
- Last release01/20/2025
Documentation
Team
Joe Zhu
MaintainerShow author detailsLutz Kettner
Show author detailsRolesCompiler, Copyright holderJacob Almagro-Garcia
Show author detailsRolesAuthorDeepak Bandyopadhyay
Show author detailsRolesCompiler, Copyright holderGil McVean
Show author detailsRolesAuthorCodeCogs Zyba Ltd
Show author detailsRolesCompiler, Copyright holderYinghan Liu
Show author detailsRolesContributorUniversity of Oxford
Show author detailsRolesCopyright holder
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- Imports6 packages
- Suggests2 packages
- Linking To1 package