orient flipped reads – adapter ligation

Hi all,

I am analyzing 2x150bp paired-end amplicons that were amplified using one sample-indexed primer. The illumina adapters were attached using ligation, i.e. half the reads are in flipped orientation.

I am planning to use dada2 after demultiplexing to count individual amplicon variants. However this requires all reads in the same orientation.

Therefore: How do I flip/reverse complement reads which have the ‘wrong’ orientation (meaning sample barcode on the 3′ end)? (preferred with a command line tool)