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.
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.