In Genomic Scaffold Filling, one aims at polishing in silico a draft genome, called scaffold. The scaffold is given in the form of an ordered set of gene sequences, called contigs. This is done by confronting the scaffold to an already complete reference genome from a close species. More precisely, given a scaffold S, a reference genome G (represented as a string) and a score function f() between two genomes, the aim is to complete S by adding the missing genes from G so that the obtained complete genome S* optimizes f(S*,G). In this talk, we will consider two alternative score functions: the first aims at maximizing the number of common k-mers between S* and G (k-Mer Scaffold Filling), the second aims at minimizing the number of string breakpoints between S* and G (Min-Breakpoint Scaffold Filling). We study these problems from the parameterized complexity point of view, providing fixed-parameter (FPT) algorithms for both problems. In particular, we show that k-Mer Scaffold Filling is FPT wrt. the number of additional k-mers realized by the completion of S. We also show that Min-Breakpoint Scaffold Filling is FPT wrt. a parameter combining the number of missing genes, the number of gene repetitions and the target distance.