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genome-annotation-pipeline

separate

Orchestrates genome annotation from assembled contigs to functional annotation, forking prokaryotic (Bakta one-step, genetic-code table from GTDB-Tk) vs eukaryotic (RepeatMask -> BRAKER3 -> functional -> ncRNA), then eggNOG/InterProScan functional assignment and Infernal/tRNAscan ncRNA. Use when committing the pro-vs-eukaryotic path and the genetic-code table from taxonomy (never guessing), annotating ONLY a decontaminated QC-passed assembly (CheckM2 before prokaryotic annotation is non-negotiable), committing the evidence set (RNA-seq + protein drives BRAKER3 training), soft-masking with a curated repeat library before gene prediction, or pinning the tool + DB version for any pangenome comparison. Hands mechanism to the genome-annotation component skills; not a re-teach of any single step.

When to use

• Prokaryotic genome annotation with Bakta
• Eukaryotic genome annotation with BRAKER3
• Repeat masking with RepeatMasker
• Functional annotation with eggNOG-mapper and InterProScan
• ncRNA annotation with Infernal and tRNAscan
• Assembly QC with CheckM2 and BUSCO
• Genetic code table selection from GTDB-Tk

When not to use

• Re-teaching individual annotation steps
• Annotating non-decontaminated or QC-failed assemblies
• Guessing genetic code tables without taxonomy

Skill page

Source