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DEploid-dev / DEploid

dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
http://deploid.readthedocs.io/en/latest/index.html
GNU General Public License v3.0
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more detailed progress tracking #281

Closed shajoezhu closed 5 years ago

shajoezhu commented 5 years ago

Adding action at the end of each mcmc action

MCMC step 100% completed. MCMC step 100% completed. MCMC step 100% completed. MCMC step 100% completed. MCMC step 100% completed. MCMC step 100% completed. MCMC step 100% completed. MCMC step 100% completed. MCMC step 100% completed. MCMC step 100% completed. MCMC step 100% completed. MCMC step 100% completed. MCMC step 100% completed. MCMC step 100% completed.

shajoezhu commented 5 years ago

MCMC step 100% completed (DEploid-Lasso learning k) MCMC step 100% completed (DEploid-IBD learning proportion) Proportion update acceptance rate: 0.223881 MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_01_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_02_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_03_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_04_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_05_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_06_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_07_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_08_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_09_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_10_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_11_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_12_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_13_v3 haplotypes) MCMC step 100% completed (DEploid-Lasso learning chromosome Pf3D7_14_v3 haplotypes)