I am analyzing viral metagenomics data (Illumina Miseq) for the first time. I have used Ray 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 ?
1) De novo assemby using Ray
2) Create a personal database of all the viral ref genomes using NCBI database
3) 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 has a metagenomics mode: Ray Meta: scalable de novo metagenome assembly and profiling, more than that, it has a taxonomic profiling mode and a quantification of microbiome mode (Ray Communities) - you will have to dig into its documentation, though.
Assembling a metagenomics dataset with a genome assembler may increase the number of chimeric contigs or other artifacts.