data import - single vs paired end


I am new to Bioinformatics and QIIME 2. I am trying to analyze some 16s sequencing data. I got my sequencing done by Novogene. I have received the fastq files from them (clean reads after filtering low-quality and chimeric reads). They used the FLASh software to merge the paired-end reads to single end reads. I am not sure what command I should use for importing these files into qiime. Is it

qiime tools import
--input-path manifest.tsv
--type 'SampleData[SingleEndSequencesWithQuality]'
--input-format SingleEndFastqManifestPhred33V2
--output-path se-demux.qza


qiime tools import
--input-path manifest.tsv
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-format PairedEndFastqManifestPhred64V2
--output-path paired-end-demux.qza


The recommended method is to import the pairs of fastq files before they were joined. Unjoined data is needed for some pipelines, so this gives you the most choice. Did you get unjoined data from Novogene?

You can list these pairs of files in your manifest, then use the second option:

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