I am analyzing viral metagenomics data (Illumina Miseq) for the first time. I have used Ray (reference below) for de novo viral genome assembly before but I haven't done metagenomics analysis before.
I know that there are some tools like Metavelvet for metagenomics. But I still need to find time to learn those tools.
For now, can I do quick and dirty analysis using following method ?
De novo assemby using Ray
Create a personal database of all the viral ref genomes using NCBI database
Blast all the contigs generated by Ray against personal database.
I assume this should give me some idea about the viral genomes present in my reads. What could be the potential flaws of this method in comparison to the tools like Metavelvet that are dedicated to metagenomics?
Ray Meta: scalable de novo metagenome assembly and profiling. Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. Genome Biology (BioMed Central Ltd). 13:R122, Published: 22 December 2012