Creating Scaffolds

Creating scaffolds can be done by selecting “Write FASTA” from the tools menu. Contiguity will attempt to reconstruct sequence and remove overlapping regions between contigs using information found in the graph file or found using self-comparisons. IT IS IMPORTANT TO NOTE THAT THIS IS A “BEST GUESS” AND MAY NOT BE ACCURATE. We suggest sanity checking any scaffolds created by mapping reads back to the newly created scaffold.