Alignment of barcode sequence question

[cupidboy]

For Ion torrent data (each read is like barcode sequence followed by target sequence)

I tried to use lastz and bowtie2 in galaxy to just align the barcode sequence part onto barcode reference sequence, but there seems not to be any parameters for me to use to omit the following target sequence part. So this cause the alignment not to work.

Is there a way to do this alignment?



Thanks a lot!