ONT FASTQ App

A simple GUI application for merging, renaming, and host-depleting Oxford Nanopore fastq.gz files on the sequencing machine.

The app detects barcode folders in an ONT fastq_pass folder, lets the user enter sample names in a browser table, and creates one merged .fastq.gz file per sample. After merging, it can optionally run deacon host depletion against human or mouse indexes.

What This App Expects

An ONT run folder containing a fastq_pass directory, usually alongside folders like:

fastq_pass/
fastq_fail/
pod5/

Inside fastq_pass, the app looks for barcode folders such as:

barcode01/
barcode02/
barcode03/

Only gzipped FASTQ files are merged:

*.fastq.gz
*.fq.gz

The app concatenates gzip files directly, so it does not decompress or recompress reads during the merge.

Quick Start

Install Miniforge or Mambaforge first so conda is available, then run:

git clone https://github.com/microbemarsh/ont_fastq_app.git
cd ont_fastq_app
./ont_fastq_app

The launcher creates or updates a Conda environment named ont_fastq_app with Streamlit, pandas, and deacon. It also downloads the deacon human and mouse indexes if they are missing, then starts the Streamlit app.

App Workflow

1. Enter the ONT run folder and output folder in the sidebar.
2. Click Detect barcodes.
3. Edit the sample-name table.
4. Leave unused barcodes as NA.
5. Preview the merge plan.
6. Run the FASTQ merge.
7. Optionally run Deacon host depletion on the merged FASTQs.

Outputs

Merged FASTQs are written directly to the selected output folder:

Sample_A.fastq.gz
Sample_B.fastq.gz
ont_fastq_merge_report.txt

If deacon host depletion is run, additional outputs are written under:

deacon_host_depleted/
deacon_reports/

Each host-depleted FASTQ is named like:

Sample_A.host_depleted.fastq.gz

Settings

The launcher supports these optional environment variables:

ONT_FASTQ_APP_ENV=ont_fastq_app
DEACON_INDEX_DIR="$HOME/deacon_indexes"
ONT_FASTQ_APP_PYTHON=3.12

Example:

DEACON_INDEX_DIR=/data/deacon_indexes ./ont_fastq_app

Why Even Make This?

ONT sequencing is used by many labs without a lot of command-line support. This app gives users a browser-based way to merge, rename, and host-deplete fastq files on the sequencing PC, then upload the merged fastqs and report files to shared folders, servers, or tools like Omi for downstream analysis.