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
Reference File
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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.