Aligning my sequences to SILVA

no you do not need to train anything. You do need to download the correct sequence file, but you do not need a taxonomy file.

No, use unaligned sequences.

For any QIIME 2 command, use the --help flag to see the help documentation for that command. E.g., use:

qiime vsearch cluster-features-open-reference --help

To see the expected inputs and their descriptions. No taxonomy required.

You can also qiime tools export any of the example files in the tutorial to see what they look like on the inside — e.g., to see if that is an aligned or unaligned fasta file (you can also use qiime tools peek to see the semantic type but that only helps if you know that there are aligned vs. unaligned types. See a short list here).

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