I am working with RNA-Seq data for a virus. My collaborator gave me a predicted single contig reference which belongs to a particular genotype (let's say GenotypeA) of the virus. Now, some of my samples are from a different genotype (B,C or D) and therefore their mapping % when aligned to my predicted reference is very low (~24%) when I use STAR.
I think doing a de-novo assembly and then aligning the reads to the new reference should help me. Are there any tools which can do single contig de novo assembly? I tried Trinity but I did not get a single contig from it.