fq-manifestor: Generate QIIME 2 paired-end fastq manifest files from your browser!

fq-manifestor is alpha release software, and was collaboratively developed with AI¹.

Why is this tool needed?

Importing can be hard. This website is designed to be a starting point to assist Illumina users with importing paired-end demultiplexed fastq files for use with QIIME 2 by helping to generate paired-end fastq manifest files. We expect to deliver more fully featured utilities like this in the not-too-distant future. 🔥🔥

1 Drop your FASTQ folder

Drop the top-level folder containing your demultiplexed FASTQ files into the box below.² Your data won't leave your computer.

2 Review the preview

Adjust the pattern options if your filenames use different conventions. The preview updates instantly.

3 Download the manifest

Download and move the manifest file into the folder you dropped.

4 Run the import

cd into that folder, then run the QIIME 2 command shown below.

📂

Drop your FASTQ folder here

Pattern options

FASTQ extensions (comma-separated) Split pattern (regex; text before first match → sample ID) Forward read pattern (regex identifying forward read files) Reverse read pattern (regex identifying reverse read files) Filter pattern (optional; only include matching paths)

Manifest filename

Manifest preview

QIIME 2 import command

The manifest uses $PWD for file paths, which the shell expands to the current working directory. Move the downloaded manifest into your FASTQ folder, then run this command from that folder:

cd /path/to/your-fastq-folder

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path manifest.tsv \
  --output-path demux.qza \
  --input-format PairedEndFastqManifestPhred33V2

This utility was created using Claude Code (claude-sonnet-4-6).
If your sequence data is on a different computer than the web browser that you're using to access this page, it's probably not possible to drag and drop the containing folder. You may instead be interested in the fq-manifestor command line utility. Learn more here.