Recommendations needed - High-throughput PCR product confirmation (500bp)

Hello all, I am performing PCR on about 1000 bacterial isolates (lysis solution only, no DNA extraction) for a culturomics project. PCR will amplify V1-V3 of 16S gene and then sending these out for sequencing to identify each isolate. I am searching for alternatives to running a small aliquot of each PCR product on a large gel. I know there are some microfluidic systems, chips, whatnot but I am unsure of the technology/machinery needed for this type of testing. I just need to make sure there is an amplicon in each sample of about 500bp but have lots of samples. Perhaps just running some big gels is still the best method ? Thanks in advance!