BodneyC / treenome

Tree-based approach to de novo DNA assembly

TreeNome

Repository containing the source code of a new approach to de novo genome assembly.

Where most current assembly techniques and algorithms make extensive use of graphs (overlap and De Bruijn mostly), TreeNome is a tree-based approach which chooses the most likely base to follow the sequence before it.

Compilation

The project is compiled with the makefile:

$ make

It should be noted that the project requires C++11.

It should also be noted that the project uses TCLAP for command line parsing, it is included in the repo as it isn't that large and saves the hassle of having to acquire it one's self.

Usage

TreeNome can currently take a fastq file and produce a set of trees, representing all paths staring with each base, and build a sequence using the algorithm; it should be noted that the accuracy of the algorithm cannot be confirmed at this stage. The program can store these trees to a file and read that file back in to construct the trees once again.

Command Format

The program requires a file, either fastq (-f) or TreeNome output file (-l).

An example command (using the example FASTQ file in ./fastq/) would be as follows:

$ ./TreeNome -f ./fastq/example.fastq -s ./data_out/out1.gno 

The TCLAP --help output should explain the rest of the switches.

$ ./TreeNome --help

USAGE: 

   ./TreeNome  {-f <string>|-l <string>} [--score-sys <Phred+33|Phred+64
               |Solexa+64>] [--thresh <0 to 1>] [-t <int>] -s <string>
               [--store-tree <string>] [-a] [-o] [--] [--version] [-h]


Where: 

   -f <string>,  --fastqfile <string>
     (OR required)  Input file in fastq format
         -- OR --
   -l <string>,  --load-file <string>
     (OR required)  Input file which was previously outputted from TreeNome


   --score-sys <Phred+33|Phred+64|Solexa+64>
     Scoring system. Phred+33 default (Sanger)

   --thresh <0 to 1>
     Threashold value

   -t <int>,  --threads <int>
     Number of threads to use

   -s <string>,  --store-sequence <string>
     (required)  File in which to store the sequence data

   --store-tree <string>
     File in which to store the tree data

   -a,  --analyse
     Perform tree analysis

   -o,  --stdout
     Print to stdout

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.


   Tree based de novo DNA assembler