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

[Man (Tamang)]

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
Man
UQ Australia

[Nicholas_Bokulich]

Hi @Man ,

@Man

Can I get the help in identifying which commands do I have to use for importing and denoising these merged fastq files?

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:

q2-fondue: Plugin for (meta)data retrieval from SRA

q2-fondue: (meta)data retrieval from SRA made simple Hello QIIMErs! On behalf of the Bokulich Lab team I would like to present to you our brand new plugin: q2-fondue (Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere)! q2-fondue allows you to grab any sequence data from the Sequence Read Archive (SRA) and corresponding metadata, given a list of SRA run accession IDs or BioProject IDs. Naturally, the resulting artifacts can then be directly plugged into …

Good luck!