I encountered small questions when analyzing AD patients' blood DNA NGS data. After mapping sequencing data to hg19 genome, I want mapping the remaining unmapped reads to viral genome. I found viral genome reference on ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/, but there are 3 files (viral.1.1.genomic.fna.gz, viral.2.1.genomic.fna.gz, viral.3.1.genomic.fna.gz).
I merged these 3 files and using blast to mapping unmapped reads to the reference. Is it right?
The mapping is so slow(20 cores dealing with 20000000 reads). Does anyone knows any methods to do this faster?