The abundance of repeat elements in genomes can impede the assembly of a single sequence. The tool Scaffold_builder was designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome.
Contigs File
.Upload File
URL
Reference File
.Upload File
URL
Prefix output files
Length of terminus that will be aligned
Minimum identity for merging contigs
Minimum length for ambiguously mapped contigs
Maximum gap length allowed
Dictates behavior for rearrangements
0: place end-to-end
1: create new scaffold sequence
 

If you use Scaffold_builder in your research, please cite:

Silva GG, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA: Combining de novo and reference-guided assembly with scaffold_builder. Source Code Biol. Med. 2013, 8:23.