Analysis of fastq files

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Hi @RENUKA! @colinbrislawn is correct: we don’t have direct/official support for nanopore sequence data and it isn’t something we’ve explored yet. If you want to experiment with these data in QIIME 2, here’s what I’d recommend:

  1. Since your FASTQ file(s) are multiplexed with barcodes in the sequences, demultiplex them following the instructions in the q2-cutadapt Community Tutorial.

  2. Perform some quality filtering on the demultiplexed sequences using q2-quality-filter.

  3. Dereplicate the sequences and cluster them into OTUs following the instructions in the q2-vsearch OTU picking Community Tutorial.

  4. Optionally perform chimera filtering following the instructions in the chimera filtering tutorial.

Note: DADA2 is currently not suitable for nanopore data. I’m unsure whether Deblur is appropriate for these data. @wasade or @antgonza, what are your recommendations for Deblurring nanopore data?

@RENUKA, if you haven’t already, I highly recommend working through the Getting Started guide and the Moving Pictures tutorial to gain familiarity with QIIME 2.

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