Differences between paired-end import formats

Hi, I have imported with qiime2 (q2cli version 2018.11.0) some paired end microbiome data generated using a Miseq Illumina machine and demultiplexed using bcl2fastq (paired fastq files have names such as: PLate1_A10_S10_L001_R1_001.fastq.gz and PLate1_A10_S10_L001_R2_001.fastq.gz, respectively), as follows:

qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path FASTQ/ --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path QIIME2-OUTPUT/microbiome-demux-paired-end.qza

assuming that my data generated from illumina reads using bcl2fastq are in Casava 1.8 format.

This command runs with no problem (no errors) and I can later use demux summarise to visualise info about my data (including per position sequence quality etc.). Results appear reasonable (to me). However, when I look at the data format (either using ‘qiime tools peek microbiome-demux-paired-end.qza’ or in the provenance graph in the qiime2 view interface) I see that my data format is given as “SingleLanePerSamplePairedEndFastqDirFmt”. I suspect that SingleLanePerSamplePairedEndFastqDirFmt (I could not find out what exact format that would be) is a more general format category that also includes as a special case CasavaOneEightSingleLanePerSampleDirFmt and that qiime reports only the higher level format. Could you please confirm if this is the case? Or, rather do I need to re-run import using SingleLanePerSamplePairedEndFastqDirFmt as input format and a manifest file?

Thank you for your help and for making available to the community this fantastic package.

Hi @mpunta!

Yes, I can confirm that is the case. There is a little bit of discussion on the matter here: How Data is Stored — QIIME 2 Developer Documentation documentation

It isn't a "higher level" format, it is just the DirectoryFormat that is associated with that particular Semantic Type.

No, you should be good to go!

Keep us posted!

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Great! Thanks a lot for the help!

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