I have a draft fungal genome assembled/scaffolded with spade (ca. 1,400 scaffolds), which I plan to submit to EMBL. However, ca. 150 of them with very short length (200-500 bp) are identified as repetitive contigs when I used nucmer/funannotate for sanity check before gene prediction. Should I exclude the repetitive scaffolds from the submission?
All suggestions are highly appreciated!