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                   EBD-scaffolder
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Description
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EBD-scaffolder is a tool for scaffolding (i.e., ordering and orienting) the contigs of a given target genome based on a given reference genome.

Prerequisite Software Components
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You will need the following tools to run EBD-scaffolder. Ensure that their paths are added to your environment:
1. Sibelia (https://github.com/bioinf/Sibelia)
2. Gurobi (https://www.gurobi.com/)
3. Python3

Download
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Thanks for downloading EBD-scaffolder.

To Compile
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Run the following command to compile EBD-scaffolder. Note that after downloading Gurobi or changing your Gurobi version, you should compile first.

Command: make

To Run
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Use the following command to run EBD-scaffolder:
./EBD-scaffolder -t [TARGET GENOME PATH] -r [REFERENCE GENOME PATH] -o [OUTPUT DIRECTORY] -s [SIBELIA CONFIGURATION] -m [THE PARAMETER M FOR SIBELIA] -T [#THREADS FOR ILP] -i [TIME LIMIT]


Parameters:
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- TARGET GENOME PATH:
  This is the path to your target genome (multi-FASTA format).

- REFERENCE GENOME PATH:
  This is the path to your reference genome (multi-FASTA format).

- OUTPUT DIRECTORY:
  This is the directory for the output files.

- SIBELIA CONFIGURATION:
  This is the parameters set for Sibelia. We provide three parameter sets in the “parameter” folder: “paraset_bacterial”, “paraset_plant”, and “paraset_human”. You can customize your own parameter set. Refer to this link (https://github.com/bioinf/Sibelia/blob/master/SIBELIA.md) for more details.

- THE PARAMETER M FOR SIBELIA:
  This parameter sets the “minimum block size” in Sibelia. The default value is 70 in our program.

- #THREADS FOR ILP:
  The number of threads for Scaffolding ILP. The default value is 1.

- TIME LIMIT:
  The time limit (in seconds) for Scaffolding ILP.

Output
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The scaffold result will be placed in “[OUTPUT DIRECTORY]/ScaffoldResult”.

Example
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Example command: ./EBD-scaffolder -t target.fna -r reference.fna -o Results -s parameter/paraset_bacterial -m 50 -T 16 -i 14400

Contact Information
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Corresponding author: Prof. Chin Lung Lu (Email: cllu@cs.nthu.edu.tw)

