Description

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.

In the phase 2 (CISA2):

• The uncertain regions located in the end of contigs were clipped (clip_info)
• The clipped out sequences are recorded in the file of clip_out
• The unalignable gaps are recorded in the file of Gaps, and the gaps of larger than 95th quantile (R2_gap=0.95) are clipped.