Future updates/fixes to consider!

[raufs]

This issue/ticket is to track ideas for downstream improvement of the suite:

• Extract more information from HyPhy reports to include in the consolidated spreadsheets.
• Add options for skani sketching/searching, in particular for marker k-mer compression factor. #75
• - Switch to pyhmmer in annotation step for HMM based databases to more effectively use available threads. #18
• By default highly similar genes in a gene-cluster which do not exhibit similarity to genes from other gene-clusters are regarded as paralogs and thus partitioned into separate ortholog groups. Consider merging such cases into a common ortholog group if high sequence similarity exists.
• Incorporate an option for automatic visualization options for dereplicated gene cluster instances in zol (e.g. using pygenomeviz or clinker) #76
• Correct FASTA output for near-core representative proteins for fai parameter suggestions in zol and handling of cases when 0 or only 1 core proteins are found (will be addressed in v1.5.6).
• Add flag to avoid replacing start proteins with M if they are instead L or V based on direct translation (implemented with bacteria in mind) if eukaryotic analysis is being performed (will be addressed in v1.5.6).
• Correct generateSyntenicVisual.py usage with new setup which generates R scripts (will be addressed in v1.5.6).
• Update cgcg to also work with results from "domain mode".
• Add options to control inflation parameter for MCL and to perform simple single-linkage clustering for ortholog group delineation.

Please feel free to add suggestions or make pull requests if you want to implement them yourselves!