How do I filter the annotated genome ?

Question

[sunnykevin97]

Hi,

Sequencing data - Illumina NextSeq 500, 150 bp RL and PE reads.

I had the masked fish genomes, using BRAKER2 by providing the vertebrate protein sequences as a hints file. I annotated the genomes. In one of the fish genomes, I had around ~85590 amino acid sequences corresponding to the ~85590 coding sequences (cds).

Please answer my questions -

How do I find the -

 1. Full length protein coding sequences ?
 2. Partial length protein coding sequences ?

And also,
3. What is the criteria for filtering out the fragmented genome assemblies ?
4. What is the min contig size cutoff for excluding the small contigs from genome assembly.

   Suggestions appreciated.