Hello @eDNA,
From the docs:
QIIME 2 currently supports importing the QIIME 1
seqs.fnafile format, which consists of a single FASTA file with exactly two lines per record: header and sequence. Each sequence must span exactly one line and cannot be split across multiple lines. The ID in each header must follow the format<sample-id>_<seq-id>.<sample-id>is the identifier of the sample the sequence belongs to, and<seq-id>is an identifier for the sequence within its sample.
So as long as you create one fasta file, with each sequence annotated with both the sample that it belongs to and a unique sequence identifier, you will be good to go.
Would it work if I change the header for example, from ">A01433:283:HFLV7DSX5:4:1204:9706:34585" to ">I7_05 A01433:283:HFLV7DSX5:4:1204:9706:34585"?
Almost. What should work is: l7_05_<sequence identifier> <everything else...>, and you repeat this pattern for each different file (sample). For the sequence identifier part it seems like you can use the current fasta headers that you have.