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I've amended the option list for the kraken2 script with a new option interleaved and updated the usage. Interleaved allows for paired reads to be supplied in a single file and utilizes the existing hooks (-S) for doing this in classify.cc. This would directly address #670 and potentially address #669. These are very superficial changes but allow for paired reads to be passed via a pipe, a very useful but previously incompatible approach. I've tested the output versus passing the paired read files directly to Kraken2 and the results are identical.