sequana-pacbio-qc 1.1.0

QC on various type of pacbio data

This is the pacbio_qc pipeline from the Sequana project

Overview:

Quality control and analysis for PacBio long-read sequencing data (BAM files). Generates comprehensive statistics on read quality, length distribution, and GC content, with optional taxonomic classification.

Input:

BAM files from PacBio sequencers (raw subreads, CCS, or processed reads)

Output:

Per-sample HTML reports with interactive visualizations, quality metrics, and optional taxonomic classification; comprehensive summary report with all samples

Status:

production

Documentation:

This README file, the Wiki from the github repository (link above) and https://sequana.readthedocs.io

Citation:

Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352

Installation

Install via pip:

pip install sequana_pacbio_qc

Optional dependencies:

• kraken2: For taxonomic classification (optional, disabled by default)

• graphviz: For DAG visualization

• apptainer: For containerized execution of tools

Quick Start

# Display help
sequana_pacbio_qc --help

# Create pipeline in current directory
sequana_pacbio_qc --input-directory /path/to/bam/files

# With optional Kraken taxonomy
sequana_pacbio_qc --input-directory /path/to/bam/files --do-kraken --kraken-databases /path/to/kraken/db

# Using apptainer containers
sequana_pacbio_qc --input-directory /path/to/bam/files --apptainer-prefix ~/containers

This creates a pacbio_qc directory containing the pipeline and configuration files.

Execution

Execute the pipeline:

cd pacbio_qc
bash pacbio_qc.sh

Or with custom Snakemake parameters:

snakemake -s pacbio_qc.rules -c config.yaml --cores 4 --stats stats.txt

Or use the sequanix graphical interface.

Configuration

The pipeline uses config.yaml to control:

• Input data: BAM file directory and pattern matching

• Kraken: Optional taxonomic database paths (disabled by default)

• MultiQC: QC report options

• Apptainer: Container image URLs (optional)

Pipeline Overview

Workflow Details

The pipeline performs the following analyses on PacBio BAM files:

1. Quality Metrics: Computes read length statistics, GC content distribution, and signal-to-noise ratios

2. Visualizations: Generates histograms and scatter plots for quality assessment

3. Per-Sample Reports: Creates individual HTML reports for each sample with:

   • Read length distribution histograms

   • GC content analysis

   • SNR (signal-to-noise ratio) metrics

   • Quality overview with sample statistics

4. Taxonomy (Optional): Performs taxonomic classification using Kraken2 when enabled

5. Summary Report: Generates a comprehensive HTML summary with:

   • Overview of pipeline and all samples

   • Summary statistics table with links to per-sample reports

   • MultiQC aggregated quality metrics

Note: Kraken2 databases are not provided with the pipeline. This step is optional and disabled by default.

Changelog

Version	Description
1.0.1	HTML reports with pipeline overview; race condition handling for parallel execution with –apptainer-prefix; improved CI/CD workflows
1.0.0	Uses latest wrappers and graphviz apptainers
0.11.0	Release to use latests sequana_pipetools framework
0.10.0	Update to use latest tools from sequana framework
0.9.0	First release of sequana_pacbio_qc using latest sequana rules and modules (0.9.5)

Contribute & Code of Conduct

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.

Rules and configuration details

Here is the latest documented configuration file to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.