running multiple samples at once

[Hannah Vollmer]

Is there a way to run multiple samples through PEAR at the same time?  I plan on demultiplexing my sample pools first, then running through PEAR, and then assembling using iPyrad.  The purpose of this order is to be able to discard any samples that don't reach a minimum threshold of PEAR assembly before continuing down the pipeline.  I have 336 samples to individually run through PEAR. Is there any way to do them all at once?

For example, my files are: 

HV001_R1_.fastq.gz

HV001_R2_.fastq.gz

HV002_R1_.fastq.gz

HV002_R2_.fastq.gz

etc.

Thanks, Hannah