A collection of workflows designed to annotate elements of the genome. These include repeat regions, protein-coding genes, ncRNA, miRNA.
Public web page: Not specified
Organisms: Not specified
ANNOTATO - Annotation workflow To Annotate Them Oll
ERGA Protein-coding gene annotation workflow.
Adapted from the work of Sagane Joye:
The following programs are required to run the workflow and the listed version were tested. It should be noted that older versions of snakemake are not compatible with newer versions of singularity as is noted here: https://github.com/nextflow-io/nextflow/issues/1659.
conda v 23.7.3
Collection of de-novo genome assembly workflows written for implementation in Galaxy
Input data should be PacBio HiFi reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads
Executing all workflows will output two scaffolded haplotype assemblies and the complete QC analyses
Please run the workflows in order: WF0 (there are two, one for HiFi and one for Illumina HiC), WF1, WF2, WF3, WF4