Description

Revision as of 05 May 2012 01:44 by admin (Comments | Contribs)

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.