Graph Coloring via Neural Networks for Haplotype Assembly and Viral Quasispecies Reconstruction

The pseudocode for the NeurHap-refine is as follows: Algorithm 1: The Local Refinement Algorithm NeurHap-refine. Two categories of datasets are used in the paper, Polyploid species and Viral Quasispecies . BW A-MEM [Li, 2013] is used to align reads to the reference genome. The detailed command is (take the 15-strain ZIKV as an example): $ ./bwa Vikalo, 2020a,b] to derive the SNP matrix from the above alignment to ensure a fair comparison.