dbg

Naive de Bruijn graph implementation in python. This is the supporting code for the blog post http://pmelsted.wordpress.com/2013/11/23/naive-python-implementation-of-a-de-bruijn-graph/.

A sample fastq file is provided and the code should be run with

python dbg.py 31 read_1.fq ...

where 31 is the k-mer size and read_1.fq ... the input FASTQ files.

The output is a GFA file

Any GFA file can be converted into a dot file using

python gfa2dot.py [file]

which will read the file (or stdin if no file is given) and produce a dot file.