Illumina 16S paired end sequence files

I have files that were analyzed a couple of years ago in QIIME1. They have separate forward, reverse and barcode fastq files.

How to perform split_libraries_fastq in QIIME2. Documentation says it has been replaced with demux emp-paired? which seems to be a type with fixed format meaning plugin is looking for specific names of the files (forward, reverse, barcodes) vs a manifest file. Is this correct?

Good morning David,

You are correct, the split_libraries_fastq.py has been replaced by qiime tools import. Have you tried any of the scripts on this page?
https://docs.qiime2.org/2018.2/tutorials/importing/

Yep, that’s --type EMPPairedEndSequences just like you said. You can rename your files to match, then place them into the same folder.

Let me know what script you tried to run, and how well it worked for you,
Colin

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