WgLink

reconstructing whole-genome viral haplotypes using L0 + L1-regularization. WgLink is a novel tool using regularized regression to stitch together regional haplotypes into global ones. The workflow of WgLink is briefed as follows: (A) WgLink first determines local haplotypes in tiling genomic windows by applying other tools: TenSQR or aBayesQR. (B) Regional haplotypes are then stitched together to generate all possible whole-genome haplotypes using a breadth-first search which could tolerate specified SNV mismatch when extending regions. (C) The final non-zero haplotype frequencies are estimated by L0L1 regularized regression.