ERGA Assembly Galaxy Long Reads & Hi-C Pipelines (Hifiasm-solo + Purge_Dups + YaHS)

Collection of de-novo genome assembly workflows written for implementation in Galaxy

Input data should be PacBio HiFi or ONT reads and Illumina 3-dimensional Chromatin Confirmation Capture (Hi-C) reads

Executing the workflows collection will output a scaffolded primary assembly and alternate contigs, with the complete QC analyses

Please run the workflows in order: WF0', WF1, WF2, WF3, WF4

'Notice there is one for HiFi, one for ONT, and one for Illumina (WGS or Hi-C). Run according to your data.

You can test the collection with the following HiFi+HiC dataset: https://usegalaxy.eu/published/history?id=15324c427869e7fc