Assembly rookie here. I have been BLASTing some of my contigs from a de novo assembly I did, and the results are coming back with very poor query coverage. Since this is an environmental isolate, I guess it's possible that there aren't many whole genome records. I tested contigs of varying sizes (largest 338 075 nt with total read count of 35 131 and coverage of 26; down to smaller contigs in the 1500 nt range with total read count of 1647). What I want to know is what is the chance that my trouble with identification is due to a) contamination in the DNA; or b) that my assembly is so shitty BLAST can't make a match?
Thanks in advance