BODBuilder - Basic-Operational De-Bruijn graph Builder

Motivation and quick explanation

This small tool has been created as a part of NGS data analysis homework in Bioinformatics Institute :)

BODBuilder provides pipeline for constructing De-Bruijn according to its mathematical definition and also utilizes heuristics to simplify it and prune from presumably wrong connections.

Typical BODBuilder workflow:

1. Takes a single or multiple files with supported data formats (no need to explicitly specify format).
2. Builds primary oriented multigraph G - creates connections in a graph using nodes with size k and primary edges with sizes k+1 between them. Each kmer is processed simultaneously with own reverse-complement one.
3. Simplifies graph until convergence - contracts edges and creates minor graph G` of a graph G. Its property - no passing vertices .
4. Removes tips from graph (low-covered edges - user-specified threshold).
5. Tries to remove bulges from graph by removing every badly covered edge.
6. Stores graph in .dot format.
7. If option --draw is provided, draws graph in .png format.

Final graph is guaranteed to have only high-covered edges related to mean edge coverage investigated after condensing and removing tips and low-covered edges. Moreover, final graph doesn't have passing vertices.

Usage

1. Clone repository:

git clone https://github.com/Abusagit/BODBuilder.git

2. Install requirements (if needed):

pip install numpy tqdm networkx

3. Typical command:

Keep --draw to obtain picture in .png format (I assume you added tool directory to PATH or provided absolute path):

py <path_to_repository>/build_graph.py -i <input_sequence_file> [<another_sequence_file>] \
-o <output_directory> \
-k <kmer sise - odd> \
-b <lower bound of coverage for edges removing> \
--draw 

Example of graph with k=55

Arguments

Argument	Description
-h, --help	Show this help message and exit
-i, --input [fasta|fastq|fna|fa]	Path to your file(s) with data for graph
-o, --outdir [./]	Output directory
-k , --kmer-size	Size of a kmer to be used for graph building
-b , --bad_cov [100]	Threshold coverage for clipping edge
--draw	Stay with this option to get picture of a final graph
--force	Force override dir if it is`nt empty