Schematic overview of the GapFiller algorithm. (a) The input data consist of a set of scaffold sequences containing gapped nucleotides and one or more sets of paired-end and/or mate-pair reads. (b) As a pre-processing step low quality nucleotides are removed from the sequence edges, thus enlarging the gap of ten nucleotides from each side. It should be stressed that the contig ends resulting from a draft assembly often contain misassemblies. (c) Paired-reads are aligned to the scaffolds and retained if one pair aligns to a scaffold sequence (dark grey) and one pair to a gapped region (black). (d) All pairs that are estimated to fall in the gapped regions are split into k-mers and used for gap filling. (e) The gap is closed from each edge by using k-mers that present a sequence overlap of size (k-mer - 1) and one nucleotide overhang. Gaps are closed if the right and left extensions can be merged and correspond to the estimated sequence gap.