nf-core/raredisease

What nf-core/raredisease is

nf-core/raredisease is a bioinformatics pipeline designed to detect and prioritize genetic variants from whole genome sequencing (WGS) and whole exome sequencing (WES) data obtained from rare disease patients. The workflow is heavily inspired by MIP (Mutation Identification Pipeline), a framework applied to integrate genomics into healthcare settings.

The software was created through a collaboration among Clinical Genomics nodes across Sweden, including Stockholm, Gothenburg, Linköping, Örebro, and Lund, together with contributors from the Danish National Genome Center and the broader nf-core community. It addresses the computational complexity of diagnosing rare disorders by uniting a comprehensive set of callers and annotators for various variant classes into a single, automated workflow.

Built using Nextflow DSL2, the pipeline encapsulates each process within isolated Docker or Singularity containers. This architecture delivers reproducibility across diverse computing platforms, from local servers to high-performance and cloud environments.

What the pipeline does

The pipeline ingests paired-end FASTQ reads alongside a sample sheet specifying metadata such as pedigree relationships, sex, and phenotype. Preprocessing begins with quality trimming and decompression using fastp or Spring, followed by read alignment using BWA, Bwa-mem2, BWA-MEME, or Sentieon DNAseq. Alignment quality, coverage metrics, and sample concordance are evaluated with tools such as FastQC, Mosdepth, MultiQC, Picard, Sambamba, Sentieon WgsMetricsAlgo, TIDDIT cov, VerifyBamID2, NGSbits SampleGender, and Peddy.

Variant detection encompasses multiple genomic alteration types. Single-nucleotide variants (SNVs) and small indels are identified via DeepVariant or Sentieon DNAscope, while structural variants (SVs) and copy number variants (CNVs) are called using Manta, TIDDIT sv, CNVnator, GATK GermlineCNVCaller, and SMNCopyNumberCaller. Mobile elements and repeat expansions are resolved with RetroSeq, ExpansionHunter, and Stranger. Mitochondrial short and structural variants are analysed using the GATK Mitochondrial short variant discovery workflow, MitoSAlt, and Saltshaker. Detected variants are annotated with Ensembl VEP, CADD, vcfanno, SVDB query, bcftools roh, UPD, and Chromograph, and then ranked using GENMOD. Benchmarking and variant evaluation can be performed with RTG Tools.

Key facts

What you can use it for

Clinical whole genome rare disease diagnostics

Processing whole genome sequencing data from patients to identify, annotate, and score candidate pathogenic single-nucleotide and structural variants.

Mitochondrial disease investigation

Evaluating patient sequencing data specifically for mitochondrial SNVs, indels, and large deletions using dedicated mitochondrial tools like MitoSAlt, Saltshaker, and GATK.

Repeat expansion and mobile element discovery

Detecting repeat expansion loci and retrotransposon insertions in neurological or developmental conditions using ExpansionHunter, Stranger, and RetroSeq.

Trio or pedigree analysis

Utilising samplesheet pedigree configurations, unparental disomy (UPD) detection, and sex checks with Peddy to filter and prioritize inherited or de novo variants.

Run it here

The research agent runs nf-core/raredisease with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.

Strengths and limits

Questions

How to cite it

10.5281/zenodo.7995798