ReindexSupers is a module that typically forms the last step in the assembly process. It performs two reindexing steps:
- Re-assigns supercontigs with IDs based on their ungapped length. The longest supercontig becomes s0, the next longest becomes s1, and so forth.
- Re-assigns contigs with IDs based on their supercontig ID and location within the supercontig. The first contig in s0 becomes c0, the next becomes c1, and so forth. Suppose s0 contains 50 contigs; then the last contig in s0 becomes c49, and the first contig in s1 becomes c50.