Importing Merged_Reads.fq into Qiime2 pipeline


I need help with a import command for merged_reads.fq
The sequencing center has not provided individual fastq files for analysis. They sent data as merged_reads.fq format. How do I import this into qiime?

Usually I create raw reads folder that contains FASTQ files for each sample and then use this command:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path demux-paired-end.qza

How should I edit the above command for merged_reads.fq?

I would appreciate your help.

Thank you,

Hi @rr220,

Good question! Here's a really helpful answer from @cherman2 regarding importing pre-merged sequences, along with some resources for performing quality control on your data:

Hope this helps! Cheers :lizard:


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