Scaffold_builder for combined de novo and reference-guided assembly

Genome sequencing is routine, however genome assembly still remains a challenge despite the computational advances of the last decade. In particular, the abundance of repeat elements in the genome make it difficult to assemble a single complete sequence. Identical repeats shorter than the average read length will generally be assembled without issue. However, longer repeats such as transposons, insertion elements, or ribosomal RNA (rrn) operons that may extend for several kilobases cannot be accurately assembled using existing tools. The application scaffold_builder was designed to generate scaffolds – super contigs of sequences joined by N bases – from draft genomes. The application was evaluated with two newly sequenced Salmonella genomes. Availability and Implementation: scaffold_builder was written in Python and can be downloaded from http://edwards.sdsu.edu/research/scaffold_builder . Contact: [e-mail]