Importing FASTA and QUAL files

Am I able to import fasta and qual files into QIIME2? If so, how, and if not, what do I need to do to make my data useable in QIIME2?

Hi @Kitkat14! What type of sequencing data is this? For example, are these raw sequences that are still multiplexed, or are they demultiplexed sequences? Has there been any denoising or clustering of the sequences (e.g. dada2 denoising, OTU picking)?

Also, what type of sequencer was used to generate your FASTA/QUAL files? The current denoising pipeline in QIIME 2 (DADA2) is tuned to Illumina data and isn’t recommended for use with non-Illumina data. DADA2 has support for processing 454 data but that functionality isn’t hooked up to QIIME 2 yet.

Assuming you have non-Illumina sequencing data, your best option is to use a different tool to process your sequences and generate a feature table (e.g. .biom file). For example, you could use QIIME 1 to perform quality filtering, demultiplexing, and OTU picking on your sequence data and then import the resulting .biom table and representative sequences into QIIME 2. Once you have your feature table imported you’ll be able to continue with downstream analyses in QIIME 2.

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My data is in 454 format. I followed your instructions and created the .biom table and imported it into QIIME2. Thank you!

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