# Scaffolding using HiC data with YAHS This workflow has been created from a Vertebrate Genomes Project (VGP) scaffolding workflow. * For more information about the VGP project see https://galaxyproject.org/projects/vgp/. * The scaffolding workflow is at https://dockstore.org/workflows/github.com/iwc-workflows/Scaffolding-HiC-VGP8/main:main?tab=info * Please see that link for the workflow diagram. Some minor changes have been made to better fit with TSI project data: * optional inputs of SAK info and sequence graph have been removed * the required input format for the genome is changed from gfa to fasta * the estimated genome size now requires user input rather than being extracted from output of a previous workflow. Inputs: * assembly.fasta [note - scaffolding is done only one haplotype at a time. eg hap1 or primary] * Concatenated HiC forward reads in fastqsanger.gz * Concatenated HiC reverse reads in fastqsanger.gz * Restriction enzyme sequence * Estimated genome size (enter as integer) * Lineage for busco Outputs: the main outputs are: * scaffolded_assmbly.fasta * comparison of pre- post- scaffolding contact maps