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aomlomics / tourmaline

Amplicon sequence processing workflow using QIIME 2 and Snakemake
BSD 3-Clause "New" or "Revised" License
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Update fastqc_per_base_sequence_quality_dropoff.py #135

Open ksilnoaa opened 2 weeks ago

ksilnoaa commented 2 weeks ago

Update fastqc_per_base_sequence_quality_dropoff.py to work with fastq_summary.qzv output

lukenoaa commented 2 weeks ago

I agree it would be great if this script can work directly from QIIME output without running FastQC/MultiQC. The zip archive of fastq_summary.qzv does contain forward-seven-number-summaries.tsv and reverse-seven-number-summaries.tsv that contain the distribution of quality scores at each position. For example, we could have the script report at which position the 9th percentile drops below a quality score of 20.

ksilnoaa commented 6 days ago

@lukenoaa yes that's what I was thinking! Would you be able to adapt that script for that functionality? Then I can include it in the V2 workflow.