Does it make sense to, and if so, how to analyze unmapped DNA reads from a newly sequenced archeological human bone sample? 80% of genomic reads did not align to the human reference genome sequence. When assembled using SPAdes, the contigs are about 180 Mb, after blasting them with NT database with 99% identity cutoff, evalue=1.e6, coverage 98%, I get 96 hits most of which bacteria, 1 hit to sugarcane, 1 hit to coconut, and 4 hits to rice, should I consider this significant or leave them as sequence contamination. Or should I go for subspecies alignment next?
The pipeline used so far:
fastqc, trimmomatic, bwa-mem-humanref-37, unmapped bam, fastqtofasta, assembly (SPAdes), contigs, blastn(galaxy)