sense versus antisense (plus or minus) sequence alignment

Question

[a.alsayed.phd]

Please, if I have a couple of query (parts of virus genome) sequences and a couple of references sequences, what are the steps required to align them correctly;i.e, to ensure that I alighn sense with sense etc. (the same direction)?

Many Thanks

[h.mon]

What are exactly "parts of virus genome"? RNAseq reads? An assembled virus transcriptome? Could you provide more details?

[a.alsayed.phd]

DNA seqs reads - sanger sequencing of PCR products

viral capsid regions (VPs) of human rhinoviruses

[GenoMax]

All sequence aligners check both orientations when doing alignments.