Please see the most up-to-date version of this protocol on my blog at https://darencard.net/blog/.
MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.
- RepeatModeler and RepeatMasker with all dependencies (I used NCBI BLAST) and RepBase (ver