I am currently using ILLUMINA PE DNA sequence data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled (SPAdes). I am now interested in using the genetic sequences from my contigs to identify the original organism (I know it is a bacterium).
I have tried using ncbi's BLASTn on one of my contigs with default parameters, on nucleotide collection database. The contig length is about 360 000 bases long. I let the query run for 30 minutes before stopping, nothing came of it. I am assuming 360 kbp is too long.
I was thinking of maybe using a ribosomal subunit sequence (which are used in phylogenetics) to identify the species, or at the very least find the taxonomic family. Is this approach feasible? How can I identify ribosonal subunit sequence from my total sequence?
If not, what would be the best way to approach this question?