Input data and files#

khloraascaf take as input data the ones that can be generated from a previous assembly from the raw reads.

They consist on a set of contigs, enriched with some specific attributes, and a set of links between two oriented contigs.

Contigs’ attributes#

For each contig, it is necessary to provide:

  • Its identifier (string)

  • Its multiplicity (integer)

  • A score that can be interpreted as the probability the contig belongs to the chloroplast genome and repeated at least one time in it


The multiplicities and the scores can be obtained e.g. by mapping the raw reads and some specific chloroplast genes on the contigs. Be sure the data you generated can be interpreted like the above given description.

File format#

This attributes must be formatted in a tab separated values file. Each line corresponds to a contig and its attributes:



C0  1   50.72
C1  1   33.33
C2  2   15.60
C3  2   18.39
C4  1   28.67

A starter contig#

  • The identifier of the contig that starts the scaffolding.

Example: C0