Good Morning

I am very new to NGS bioinformatics so apologise in advance if I miss some of the detail. I have developed a work flow to enrich viral genomes directly from patient samples for Illumina MiSeq sequencing with the aim of determining whole genomes where possible. The virus I am targeting has a genome of approximately 36kb but has at least 104 genotypes which infect humans with up to 20% genome variation depending on the type. I have Illumina paired end reads for analysis with average fastq file size of around 30-40MB which should be exclusively viral genome reads. I have explored DeNovo assembly options but also wanted to look at the possibility of sequence alignment for my assembly as the DeNovo results I am achieving are not always favourable. I have had no issues with aligning to a single reference genome using multiple alignment tools but with 104 genotypes I wondered if there was a way to align against all 104 genotypes at once and determine a best match which I can then go back and align against in isolation for further analysis. There is no way to determine before hand which type the virus is likely to belong to and the variation can occur at multiple points along the genome so targeting a particular smaller area is not going to be helpful. There is also a possibility of discovering new viral types which may not align favourably to any of the available whole genomes or to getting samples containing more than one virus type. I appreciate I could align against each of the reference genomes individually but with several hundred patient samples this would take a significant amount of time so I was hoping there was a solution out there I was missing. I have produced a single fasta file of all of the reference genomes and tried aligning to that but aside from the sheer amount of data generated I think that most reads are only aligned once. Would using the bowtie all function get around this and allow alignment of each read to each reference it matches and if so how can I determine which reference has the most reads aligned to it easily? Any suggestions for tools or further reading which may assist me would be gratefully appreciated

Best Wishes Emma