Creating a visuaization fasta file from a .qza file

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Hey Qiime2 Community!

I am trying to create a fasta file from a .qza file. I am trying to compare a bunch of samples from different primer sets so I am trimming them first with cutadapt and then need the fasta file. I am using Qiime2 version 2024.5. I uploaded the fasta sequences with these commands:

qiime tools import --type SampleData[SequencesWithQuality] --input-path $1 --output-path 2_demux_output_file.qza --input-format SingleEndFastqManifestPhred33V2

and then trimmed the reads using:

qiime cutadapt trim-single --i-demultiplexed-sequences 2_demux_output_file.qza --p-adapter TTACCGCGGCKGCTGRCAC ATTAGAWACCCBNGTAGTCC --p-match-read-wildcards --p-match-adapter-wildcards --verbose --o-trimmed-sequences trimmed_remove_primers_wild.qza

qiime cutadapt trim-single --i-demultiplexed-sequences trimmed_remove_primers_wild.qza --p-front GTGYCAGCMGCCGCGGTAA GGACTACNVGGGTWTCTAAT --p-match-read-wildcards --p-match-adapter-wildcards --p-discard-untrimmed --verbose --o-trimmed-sequences primers_removed_final.qza

And then I try to visualize it with:

qiime demux summarize --i-data primers_removed_final.qza --o-visualization trimmed_4_demux_output_visfile.qzv

But this does not provide me with the fasta file. I do not want to run DADA2 or Deblur on the sequences (I know how to get sequence files after running those commands) because I just want to look at them post trim from this file. How to I get the fasta file from primers_removed_final.qza? I don't need the count file or anything. Just the fasta file created. Any help would be greatly appreciated. Thanks

Hannah

2

Hello @hdoris,

Your data is actually in fastq format not fasta format as a demux. Denoising/dereplicating is what gives you fasta files. If you want just these fastq files you can use the qiime tools export command.

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