Fully Dynamic De Bruijn Graph

The code helps in creating a dynamic de bruijn graph, supporting both addition/deletion of nodes from it while taking a minimal memory space.

System Requirements :

• OS : Linux (Tested on Ubuntu 16.04 LTS) (64 BIT Version)
• ARCHITECTURE: 64 BIT
• Memory : Based on file executed. Recommeneded : Atleast 8GB.
• Compiler : g++

STEPS :-

1. Download fully_dynamic_dbg.zip from website.

2. Extract fully_dynamic_dbg.zip.

3. Open terminal(Ctrl+Shift+T in Ubuntu) and goto extracted fully_dynamic_dbg/ directory (Command : cd /home//Downloads/fully_dynamic_dbg). Or you can right click on the extracted fully_dynamic_dbg directory and click on open in terminal.

4. Run 'make' command to build binary.

5. This will generate 3 binary files:-
   5.1. dbg

   • DESCRIPTION : Used to test construction of data structure for a given fastq file as input.
   • EXECUTION COMMAND : ./dbg <input_file.fastq>
   • EXAMPLE COMMAND : ./dbg norovirus.fastq
     5.2. dbg_unit_test
   • DESCRIPTION :
     • Used for unit testing a sample fastq file already present in current directory : unit_test.fastq
     • Edit searchNodes.txt to specify what all nodes to search. (Sample nodes already present)
     • Edit insertNodes.txt to specify what all nodes to insert. (Sample nodes already present)
     • Edit deleteNodes.txt to specify what all nodes to delete. (Sample nodes already present)
   • EXECUTION COMMAND : ./dbg_unit_test
   • EXAMPLE : ./dbg_unit_test
   • Can open generated unit_test_debruijn.txt to see the De Bruijn Graph.
     5.3. norovirus_test
   • DESCRIPTION : Used for testing construction of datastructure for norovirus.fastq input file.
   • EXECUTION COMMAND : ./norovirus_test
   • EXAMPLE : ./norovirus_test
   • Can open generated norovirus.txt to see the De Bruijn Graph

6. For any queries Contact us using our website/Contact section. https://www.dynamicdebruijnuf.com/