quality-filter q-score does not correctly process PairedEndSequencesWithQuality

I am processing paired end V3-4 16S amplicon data sequenced on a MiSeq with a V3 600bp kit. My sequencing data is poor quality and so I would like to run quality-filter q-score on my data prior to cutadapt and Dada2 [note: I know the filtering is redundant to Dada2 and that this is a regularly discussed topic].

Anyways, quality-filter q-score is not processing SampleData[PairedEndSequencesWithQuality] correctly. Everything appears to run as it should -no error messages are thrown- but the output only includes the forward read and reverse reads are discarded. I know this topic is essentially identical to qiime quality-filter q-score does not accept SampleData[PairedEndSequencesWithQuality] but that post is old and from the plugin documentation it appears as though SampleData[PairedEndSequencesWithQuality] is supported.

  • Version of QIIME 2: 2021.4 installed in a conda environment

qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path 16S_manifest.tsv
–output-path demux.qza
–input-format PairedEndFastqManifestPhred33V2

qiime quality-filter q-score
–i-demux demux.qza
–p-min-quality 12
–p-quality-window 3
–p-min-length-fraction 0.83
–o-filtered-sequences demux_qfilter.qza
–o-filter-stats stats_qfilter.qza

  • Error message?: none, but the output does not produce the expected result based on the plugin information
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Hi there @jsogin574!

quality-filter q-score only operates on single-end reads - if you provide paired-end reads, it’ll just operate on the forward reads. This could be made more clear in the documentation, sorry about that.

This pattern pops up all over QIIME 2 - many methods accept paired-end reads as input, such as dada2 denoise-single - if you hand it paired-end reads, that particular method will just operate on the forward (single) reads.

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Ah. Got it. Thank you @thermokarst

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