CISA consists of four phases for contig integration.
Four folders are generated after running CISA.
In the phase 1 (CISA1):
- The representative contigs and their explained contigs are recorded in the file of Explained.txt.
- Information about contig extensions are recorded in the file of Extend_info.
- For example,
- Head: >Skeleton contig >Extended contig
- Tail: >Skeleton contig >Extended contig
- The processed contigs named R1_contigs.fa is placed outside the CISA1 folder.