How to directly import merged fastq files downloaded from NCBI SRA?

Hi QIIME2 team, I have been downloading already merged fastq files (forward and reverse merged into one fastq file) from the NCBI SRA database. Can I get the help in identifying which commands do I have to use for importing and denoising these merged fastq files? Thanks
UQ Australia

Hi @Man ,

These files from SRA contain both the forward and reverse reads in a single file — you need to separate these reads before importing to QIIME 2. QIIME 2 does not have any actions for splitting these reads.

However, you could use q2-fondue to automatically download and import data from SRA. This plugin will perform the read splitting, but only as part of the download process. So I highly recommend using this for retrieving data from SRA:

Good luck!


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