This repository contains various scripts that I have created that are useful for genome annotation (repeats & proteins). They may exist in some form already elsewhere, but they are here in case others need them. In particular, they are used in a MAKER tutorial I created, which I have heard others reference a lot.
I try to provide more details and usage information at the beginning of each script. Here is a quick description of what each script does for reference. User beware: these scripts have not been extensively tested and may not perform as desired, and as such, they are provided as-is, with no support and no guarantee of proper or desirable functioning.
genestats: calculates several count/length statistics for gene models in a GFF3 file
ncbi2uniprot: renames the header lines of an NCBI protein FASTA file so that they are very similar to the standard UniProt FASTA headers
ncbi_CDS_creator.sh: creates a CDS file from a NCBI genome using the feature table
orthorbb: infers homology between a query and a reference set of protein sequences using reciprocal and one-way best BLAST searches
rmOutToGFF3custom: converts the .out file from RepeatMasker to a "better" GFF3 file than default script in RepeatMasker