QIIME1 Pandaseq and Importing

Hi, again.

I have so many samples to analyze, and old samples remain in FASTA format forward-reverse-merged with PandaSeq. Because QIIME1 needs only FASTAs and we have to save storage volume. So we don’t have FASTQs in some samples, shortly, they don’t have quality score info.

The things I want to ask are,

  1. How can I import FASTA set? Exactly saying, What on earth is importing type and format? The FASTAs came from merging each forward FASTQ with reverse one using PandaSeq, already trimmed and quality controlled.
  2. When I import the FASTA set, what phase do I start at in the manual “Moving Pictures” tutorial, alignment, denoising or other? At last time after I used deblur-denoise, no triming(–p-trunc-len 0), could not progress to next level, saying “my sequences longer than…(whatever)”(don’t remember).

Please let me know.

Hey there @Seok_Jun_Kim!

What do these FASTA files represent? Are they individual features, or are they somehow associated with a sample?

If you can get these FASTA into the QIIME 1 seqs.fna format, you could try following this guide.

Really helpful. U R the BEST!

So, “.fna” format is the output file that come from add_qiime_labels.py in QIIME1, right?

Sorry, I missed that comment. The FASTAs I refered represent individual 16S rRNA sequences(V3-V4 region) of each patient's fecal microbiome sample from merging both forward and reverse FASTQs with PandaSeq, sequenced by Illumina MiSeq.

I am not a QIIME 1 developer, so I will defer to someone like @antgonza or @wasade to confirm, but after reading this resource, I think the answer is "yes".

Hi @Seok_Jun_Kim,

add_qiime_labels.py should work.

Let us know how it goes.


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