Welcome to Fada

This pipeline, under development at Clinical Genomics Uppsala, is used to call variants from long-read data from rare disease patients.

You can find the github repository at https://github.com/clinical-genomics-uppsala/fada/

Fada is a snakemake pipeline that is built using modules from Hydra Genetics to process long-read .bam files from Pacbio Revio and Oxford Nanopore Technologies (ONT) R10 data.

If Snakemake is new to you a good place to start is doing the snakemake tutorial.

Hydra-Genetics Modules

The current module versions (as configured in config/config.yaml) are:

• alignment v0.7.0: Read alignment and mapping tools
• annotation v1.4.0: Variant annotation and functional analysis
• cnv_sv v1.0.1: Copy number variant and structural variant detection
• compression v2.1.0: File compression and format conversion
• filtering v1.1.0: Variant filtering and quality control
• misc v0.3.0: Miscellaneous utilities and helper functions
• prealignment v1.4.0: Pre-processing and quality control of raw reads
• qc v0.6.0: Quality control metrics and reporting
• reports v1.1.0: Report generation and visualization
• snv_indels v1.2.0: Small variant (SNV/indel) detection and genotyping

Each module is maintained as a separate repository within the Hydra-Genetics organization and can be updated independently. Version pinning ensures reproducible analyses.

Supported Workflows

PacBio Twist Cancer Panel

Targeted enrichment analysis for a hereditary cancer panel

• Targeted SNV INDEL calling
• CNV detection
• SV calling in target regions

PacBio Whole Genome Sequencing (under development)

This pipeline is currently used only for testing and development, we recommend the GMS Nallo pipeline for a comprehensive long-read WGS rare-disease pipeline

WGS analysis including:

• Genome-wide SNV and INDEL calling
• Genome-wide SV and CNV detection
• STR expansion detection

ONT Targeted STR Analysis (under development)

Specialized workflow for short tandem repeat analysis with targeted ONT data:

• STR expansion detection
• STR expansion annotation
• High-resolution repeat visualization