I have just aligned a paired-end FastQ (R1 & R2) files to a published viral genome using Bowtie2. The end goal is to extract the aligning reads from this sample and obtain a consensus sequence. Then I'd like to eventually compare that sequence to a reference sequence (published) to compare the differences between the two (I basically want to see if there is any nucleotide variation between the two samples), to help with primer design.
So, I have never done this type of pipeline before and would just like some assistance on creating and obtaining a consensus sequence. I use usegalaxy.eu and not coding.