Is there a standard definition for "assembly polishing" in the field?
Is there a standard definition for what polishing algorithms do?
My understanding of "polishing" is strongly influenced by Pilon:
Whereby users input a reference FASTA along with the BAM of aligned reads against this reference FASTA. The polishing algorithm then does alignment to discover local misassemblies and other alignment inconsistencies. These are then "corrected", i.e. "polished".