- Organizing inputs: Naming genomes and RNAseq reads
- Mapping RNAseq reads to the genome (STAR)
- Calculating genome quality metrics (Assemblethon, BUSCOs) - seprate alt-haplotypes in genome, if any.
- Remapping RNAseq reads to primary scaffolds/contigs only (STAR)
- Running transcript assembly (Cufflinks, Strawberry, Stringtie, Class2 and Trinity), Splice junctions (Portcullis)
- Run ab initio gene prediction (BRAKER)
- Map Trinity to genome to generate GFF3 (GMAP)
- Pick transcripts for evidence-based predictions (Mikado)
- Combine annotations (Mikado and Homology based predictions with ab initio) (GeMoMa)
- Identify primary transcripts (TRaCE)
- Finalize GFF3 files (custom) and calculate annotation metrics (AGAT, BUSCO)
- Perform repeat annotations (EDTA)
- Functional Annotations (TBD)