Import merged fastq files via manifest

[arwqiime (ARW)]

Hello Qiime2 experts,
I have a set of fastq.gz files of 50 environmental samples; they are already demultiplexed, primer-clipped and merged by BBmerge. I thought I should be able to import them using this procedure, but there are two points where I’m not sure whether I have used the correct specification (marked with ### below)

qiime tools import
–type ‘SampleData[SequencesWithQuality]’ \ ### is this correct for fastq.gz files
–input-path Manifest.csv
–output-path import_results.qza
–source-format FastqGzFormat

Manifest.csv
sample-id,absolute-filepath,direction
sample-1,$PWD/some/filepath/sample1_merged.fastq.gz,forward ### should it be ‘forward’ or 'merged’
etc.

Thank you for your suggestions!
Alfons

[Mehrbod_Estaki]

Hi @arwqiime,
If you are planning on using dada2 in qiime2 it is better to import your reads unjoined as dada2 performs denoising on individual reads and then merges them. See this thread where a similar question was discussed.
If your plan is to use another method such as vsearch, I think this tutorial can help with your importing questions. Specific to your question, see the

Importing pre-joined reads

section.

Hope that helps!