Alignments refer to pairs of sequence. Once you know how a pair of sequences go together, you can look at stringing the pairs along into a contig. The contig is essentially the consensus sequence that is produced from the components.To create a contig, we use the steps shown on this slide.What are switch points? As you create the consensus sequence of the contig, the switch points tell you where to stop using the sequence from one component and begin using the sequence from the next.
AssemblyUnderstanding the human reference genome Deanna M. Church Staff Scientist, NCBI 26 Mar 2013
Build sequence contigs based on contigsdefined in TPF (Tiling Path File). Check for orientation consistencies Select switch points Instantiate sequence for further analysis Switch point Representative chromosome sequence
The human reference assembly is a COMPOSITE of many individualsThe human reference assembly is NOT staticAccession.versions are KEY to data managementWhen the reference assembly updates: Your favorite region may have the same SEQUENCE but different COORDINATES Your favorite region may CHANGE significantly We have the TOOLS to help! http://www.ncbi.nlm.nih.gov/variation