How can I process MD5sum format sequence data in the QIIME2?

Yay! :tada:

There are several options. You can use the pre-made Greengenes or SILVA classifiers that are available on the Data resources page. You can also use RESCRIPt to compile your own SILVA, or NCBI reference db.

We have plans to make it easier to import and format RDP and GTDB reference sequence and taxonomy data for use within QIIME 2. But at this time we can not provide a time frame when this will be completed. If you search the forum you'll find several threads in which others may have compiled RDP and GTDB files for use. They may be willing to share those files so that you can train your own classifier.