For a single paired end read the script is 
hisat2 -x /path/to/hg19/indices -1 sample_1.fq.gz -2 sample_2.fq.gz | samtools view -Sbo sample.bam -
Our queue is full so I'm not able to test this but is it possible to allign multiple paired end reads in one go and how would I go about it?

Probably your `sample_1.fq.gz` and `sample_2.fq.gz` **files** already contain multiple **reads** inside. I guess you want to align multiple files, right? 

But do you want the output in a single file, or multiple files as output? For the former, you can pass a comma-separated list of files to hisat2 (see `-1` and `-2` on hisat2 [manual][1]). For the later, there are several option, such as a bash loop, using Parallel, a make script, job arrays (if your queue is managed with SLURM / Torque / SGE), among others options.

  [1]: https://ccb.jhu.edu/software/hisat2/manual.shtml