Analysis of fastq files

Hi I am new to qiime2. I have a fastq file generated from nanopore sequencing of around 42 MB. I want to analyse the sequences of that file. What programs can I use. The file is already with barcode.

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Hello Renuka,

It looks like Qiime 2 did not support this kind of data last year, but maybe it does now!

Let’s see what the developers recommend!


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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.


Hi @jairideout,

Deblur has only been tested on Illumina data. I don’t know enough about the generation of amplicons with nanopore to have an intuition about the use of Deblur here, unfortunately.


My data is demultiplexed. I only have amplicon reads and now is it possible to use qiime2 for further processing. I have both fastq as well as fasta files.

Hi @RENUKA, I would recommend sticking with the steps outlined above by @jairideout, although it sounds like you can skip #1 if your reads are already demultiplexed (as in, you have on file per sample for single-end or two files per sample for paired-end, I am unfamiliar with nanopore, so I am not sure if that technology only produces one or the other). Besides those steps listed, @jairideout’s suggestion of looking at the Getting Started guide and the Moving Pictures tutorial should also help get you moving in the right direction. Please keep us posted! :t_rex:

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