BethYates

Sub-workflow for gene statistics

3

We want to be able to include some standard basic statistics on the gene/protein annotation set for an assembly in a genome note. This sub workflow should accept an annotation...

### Description of feature Add GFA stats https://github.com/vgl-hub/gfastats to the genome statistics subworkflow

Merqury and Meryl

3

### Description of feature Allow running of Merqury and Meryl as an alternative to Merqury.FK? As used by CBP and Nor-BP

### Description of feature Add GBIF to the set of sources queried by the genome metadata subworkflow

MUMmer used by Nor-BP to evaluate differences between assembly haplotypes. Is this something we want to add as an option to the genomenote pipeline?

Include GenomeScope profile in genome note?

Investigate adding Flagger to the genomenote pipeline to evaluate diploid assemblies

### Description of feature Add COPO to the set of sources queried by the genome metadata subworkflow

### Description of feature Refine input parameters and samplesheet checking ahead of release 2.0

### Description of feature Evaluate HiC maps of multiple species to try and set some suitable default values to set in the config when uploading HiC data to Higlass