Read Count in a de Bruijn Graph

Our discussion in previous sections focused on the structure of the de Bruijn graph and did not give much important to the coverage count. In case of transcriptomes and metagenomes, both the structure and the coverage count are important. A subset of assembly programs store both the graph structure and counts, but they require more memory to hold the de Bruijn graph. Highly optimized assemblers like Minia only save the k-mer sequences, but not their counts. However, it is possible to add the count information at a later stage after completing pre-assembly through an extra map stage.