Fig. 1

Schematic of GP-Target framework and steps. (1) Long-reads are first mapped to the draft assembly. (2) Then, by default, soft masked regions of the assembly are excised; alternatively, a BED file can be used to specify coordinates for the regions of interest to be excised. (3) The mapping file is modified to match the coordinate system of target regions and the resulting PAF file is passed to GoldPolish. (4) GoldPolish is run on the target regions to correct base errors. (5) The polished target sequences are re-inserted into the original assembly to yield the final polished assembly output