Seqmon

A Lightweight Sequencing Monitor

Seqmon is a web application built on Plotly Dash designed to monitor sequencing runs across multiple sequencers and analyze the statistics of demultiplexing processes.

Seqmon parses through all the paths defined in config.yaml and collects the following information:

• Run Statistics: Aggregated from both BCL and MultiQC data.
• Lane Statistics: Extracted from MultiQC data.
• Sample Statistics: Also sourced from MultiQC data.

These statistics are saved under the ./data/ directory and can be updated when new data becomes available. Existing entries won’t be reloaded unless you manually remove the associated files.

Configuration

Prerequisites

1. Clone the Repository: Begin by cloning the repository to a location where your data is stored:

   gh repo clone chaochungkuo/seqmon

2. Adjust Configuration: Update the configuration file located at config/config.yaml to reflect your environment.

   • bcl_paths: Paths to the BCL files from Illumina sequencers.
   • multiqc_paths: Paths where the multiqc_data directories can be found.

   The subfolders in these paths should correspond to the run IDs assigned by the Illumina sequencers.

   Example Data Structure:

   BCL outputs from Illumina Sequencers:
   - /data/raw/miseq1_M00818/240826_M00818_0927_000000000-KWWCM
   - /data/raw/miseq1_M00818/240902_M00818_0930_000000000-LNB62
   - /data/raw/miseq2_M04404/240708_M04404_0764_000000000-LMF2H
   - /data/raw/miseq2_M04404/240711_M04404_0765_000000000-LL9CJ
   - /data/raw/nextseq_NB501289/240815_NB501289_0844_AHT2CJBGXW
   - /data/raw/nextseq_NB501289/240820_NB501289_0846_AHH55LAFX7
   - /data/raw/novaseq_A01742/240815_A01742_0281_BHWL23DMXY
   - /data/raw/novaseq_A01742/240819_A01742_0283_BHGL5GDRX5
   
   Demultiplexing folders containing multiqc_data:
   - /data/fastq/240404_A01742_0223_AH3VMHDRX5
   - /data/fastq/240408_A01742_0224_AH3W5YDRX5
   - /data/fastq/240408_M04404_0742_000000000-LHTLJ
   - /data/fastq/240410_NB501289_0799_AHNVNJBGXV
   

   Update your config.yaml accordingly:

   bcl_paths:
     - /data/raw/miseq1_M00818
     - /data/raw/miseq2_M04404
     - /data/raw/nextseq_NB501289
     - /data/raw/novaseq_A01742
   
   multiqc_paths:
     - /data/fastq/
   
   sequencers:
     - miseq1_M00818
     - miseq2_M04404
     - nextseq_NB501289
     - novaseq_A01742

   Ensure the sequencer names in the configuration match your setup.

Deployment

Setting Up the Environment

1. Create a Conda Environment:

   Create and activate a new conda environment:

   conda create -n seqmon python=3.11
   conda activate seqmon

2. Install Dependencies:

   Install the required packages:

   pip install -r requirements.txt

Running the Application

To deploy Seqmon, run the following command:

python src/app.py

By default, the app will be served at http://0.0.0.0:8050.

Feedback and Contributions

We welcome any feedback, suggestions, or contributions. Feel free to submit issues or pull requests on GitHub.