Updated List of nf-core Pipelines (Released) Sorted by Stars (as of November 22, 2024)
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Released
- rnaseq: RNA sequencing analysis pipeline using STAR, RSEM, HISAT2, or Salmon with gene/isoform counts and extensive quality control (921 stars).
- sarek: Analysis pipeline to detect germline or somatic variants from WGS/targeted sequencing (410 stars).
- mag: Assembly and binning of metagenomes (217 stars).
- scrnaseq: Single-cell RNA-seq pipeline for 10X genomics data (214 stars).
- chipseq: ChIP-seq peak-calling, QC, and differential analysis pipeline (195 stars).
- ampliseq: Amplicon sequencing analysis using DADA2 and QIIME2 (188 stars).
- atacseq: ATAC-seq peak-calling and QC analysis pipeline (188 stars).
- naoseq: Nanopore demultiplexing, QC, and alignment pipeline (180 stars).
- fetchngs: Fetch metadata and raw FastQ files from public databases (151 stars).
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eager: Ancient DNA analysis pipeline (148 stars).
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rnafusion: RNA-seq analysis for gene-fusion detection (144 stars).
- methylseq: Methylation analysis pipeline with Bismark or bwa-meth (140 stars).
- taxprofiler: Multi-taxonomic profiling of metagenomic data (128 stars).
- viralrecon: Viral assembly and intrahost variant calling (125 stars).
- hic: Chromosome Conformation Capture data analysis (92 stars).
- raredisease: Variant analysis for rare disease patients (90 stars).
- cutandrun: Analysis pipeline for CUT&RUN and CUT&TAG experiments (81 stars).
- pangenome: Renders sequences into a pangenome graph (78 stars).
- smrnaseq: Small-RNA sequencing analysis pipeline (74 stars).
- funcscan: Genome screening for functional and natural product gene sequences (74 stars).
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differentialabundance: Differential abundance analysis (64 stars).
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bacass: Bacterial assembly and annotation pipeline (63 stars).
- hlatyping: HLA typing from NGS data (63 stars).
- proteinfold: Protein 3D structure prediction pipeline (58 stars).
- airrflow: Adaptive Immune Receptor Repertoire sequencing analysis (54 stars).
- bactmap: Phylogeny from bacterial genomes (52 stars).
- oncoanalyser: Cancer DNA/RNA analysis pipeline (50 stars).
- rnasplice: RNA-seq alternative splicing analysis (46 stars).
- demultiplex: Demultiplexing pipeline for sequencing data (44 stars).
- epitopeprediction: Epitope prediction and annotation pipeline (42 stars).
- rnavar: RNA variant calling pipeline (37 stars).
- mhcquant: Quantify MHC-eluted peptides from mass spectrometry data (33 stars).
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proteomicslfq: Proteomics label-free quantification pipeline (33 stars).
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crisprseq: Analyze CRISPR edited data (31 stars).
- isoseq: PacBio Iso-Seq genome annotation (29 stars).
- circdna: Detect extrachromosomal circular DNA (28 stars).
- readsimulator: Simulate sequencing reads (27 stars).
- imcyto: Image Mass Cytometry analysis (25 stars).
- multiplesequencealign: Multiple Sequence Alignment pipeline (22 stars).
- bamtofastq: Convert BAM/CRAM to FastQ (22 stars).
- metatdenovo: De novo assembly for metagenomics data (22 stars).
- scnanoseq: Single-cell/nuclei pipeline with Nanopore data (21 stars).
Under development
- spatialvi: Spatially-resolved gene counts for 10x Genomics Visium (52 stars).
- circrna: Quantify circRNA, differential expression, and miRNA target prediction (45 stars).
- scdownstream: Single-cell transcriptomics QC, integration, and visualization (41 stars).
- lncpipe: Long non-coding RNA analysis from RNA-seq data (under development) (33 stars).
- deepmodeloptim: Optimizes deep learning models for genomic applications (23 stars).
- gwas: Genome Wide Association Studies pipeline (under construction) (22 stars).
- genomeannotator: Gene structure identification in draft genomes (18 stars).
- phaseimpute: Phases and imputes genetic data (17 stars).
- genomeassembler: Genome assembly pipeline (16 stars).
- pathogensurveillance: Population genomics for pathogen monitoring (13 stars).
- variantbenchmarking: Benchmarking for variant-calling pipelines (premature) (12 stars).
- omicsgenetraitassociation: Multi-omic data integration for trait analysis (10 stars).
- phageannotator: Identifies and annotates phage sequences in metagenomic data (10 stars).
- tfactivity: Differentially active transcription factor identification (9 stars).
- createpanelrefs: Generate reference panels from sample datasets (8 stars).
- datasync: Automation and system operation tasks (8 stars).
- mcmicro: Processes multi-channel whole-slide images into single-cell data (8 stars).
- metapep: Processes metagenomes to epitopes and beyond (8 stars).
- variantcatalogue: Creates variant catalogues for populations (8 stars).
- tbanalyzer: Analysis pipeline for Mycobacterium tuberculosis complex (7 stars).
- radseq: Variant-calling for RADseq sequencing data (6 stars).
- meerpipe: Processes MeerKAT pulsar data for astronomy applications (5 stars).
- rnadnavar: RNA and DNA integration for somatic mutation detection (5 stars).
- spatialxe: (Details not specified) (5 stars).
- drugresponseeval: Evaluates drug-response prediction models (4 stars).
- rangeland: Analyzes satellite imagery for land-cover trends (4 stars).
- genomeqc: Compares genome quality and annotations (3 stars).
- methylarray: Processes Illumina methylation data (3 stars).
- spinningjenny: Simulates industrial revolution with agent-based models (2 stars).
- troughgraph: Quantitative permafrost landscape analysis (2 stars).
- pacvar: Processes PacBio sequencing for WGS and targeted data (updated 12 hrs ago) (1 star).
- sammyseq: Analyzes chromatin accessibility with SAMMY-seq data (1 star).
- fastqrepair: Repairs and reorders corrupted FASTQ.gz files (0 stars).
Archived
- deepvariant: Variant calling pipeline leveraging Google's DeepVariant (40 stars).
- quantms: Quantitative mass spectrometry workflow supporting DDA-LFQ, DDA-Isobaric, and DIA-LFQ (31 stars).
- scflow: RNA-seq analysis for single-cell and single-nuclei data (recommended: nf-core/scdownstream) (23 stars).
- exoseq: Exome sequencing and variant calling pipeline (recommended: nf-core/sarek) (16 stars).
- smartseq2: Processes single-cell RNA-seq data from the SmartSeq2 protocol (15 stars).
- vipr: Viral genome assembly and low-frequency variant calling (14 stars).
- denovohybrid: Hybrid genome assembly combining long and short reads (under construction) (8 stars).
- crisprvar: Evaluates genome editing experiment outcomes (WIP) (5 stars).
- ddamsproteomics: Quantitative shotgun mass spectrometry for proteomics (4 stars).
- neutronstar: De novo assembly pipeline for 10X linked-reads using Supernova (3 stars).
- ssds: Single-stranded DNA sequencing pipeline (1 star).
- liverctanalysis: Pipeline for liver CT image analysis (under construction) (0 stars).