airrflow
nf-core/airrflow
B and T cell repertoire analysis pipeline with the Immcantation framework.
Proteomics & immunology110 params5.1.2
Pinned Oct 10, 2026
The collection
All pipelines
95 nf-core pipelines, each pinned to a release and documented from source. Search by name or tool, or narrow to a research domain.
95 pipelines
- ampliseq
nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Microbial & metagenomics178 params3.1.0Pinned Oct 28, 2026
- atacseq
nf-core/atacseq
ATACSeq peak-calling and differential analysis pipeline.
Epigenomics88 params2.1.2Pinned Aug 7, 2023
- bacass
nf-core/bacass
Simple bacterial assembly and annotation
Microbial & metagenomics76 params2.7.0Pinned Nov 3, 2026
- bacmodel
nf-core/bacmodel
Systems-based bacterial functional modeling pipeline
Microbial & metagenomics46 params1.0.1Pinned Oct 30, 2026
- bactmap
nf-core/bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Microbial & metagenomics39 params1.0.0Pinned Jun 18, 2021
- bamtofastq
nf-core/bamtofastq
Workflow converts one or multiple bam/cram files to fastq format
Data & utilities35 params2.2.1Pinned May 13, 2026
- callingcards
nf-core/callingcards
An automated processing pipeline for mammalian bulk calling cards experiments
Epigenomics53 params1.0.0Pinned May 24, 2024
- chipseq
nf-core/chipseq
ChIP-seq peak-calling and differential analysis pipeline.
Epigenomics82 params2.1.0Pinned Oct 7, 2024
- circdna
nf-core/circdna
Pipeline for the identification of circular DNAs
Genomes & evolution58 params1.1.0Pinned Feb 10, 2024
- coproid
nf-core/coproid
COPROlite host IDentification
Microbial & metagenomics39 params2.0.1Pinned Feb 16, 2026
- createpanelrefs
nf-core/createpanelrefs
Generate Panel of Normals, models or other similar references from lots of samples
Variant calling61 params1.1.0Pinned Nov 3, 2026
- createtaxdb
nf-core/createtaxdb
Parallelised and automated creation of metagenomic classifier databases of different tools
Microbial & metagenomics73 params3.1.0Pinned Jul 3, 2026
- crisprseq
nf-core/crisprseq
Pipeline for the analysis of CRISPR data
Genomes & evolution58 params2.3.0Pinned Nov 8, 2024
- cutandrun
nf-core/cutandrun
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis.
Epigenomics103 params3.2.2Pinned Feb 1, 2024
- datasync
nf-core/datasync
A simple sysops pipeline that can be used to synchronize, integrity check and permanently archive data.
Data & utilities29 params1.0.2Pinned Oct 6, 2026
- demo
nf-core/demo
An nf-core demo pipeline
Data & utilities30 params1.2.0Pinned Jun 24, 2026
- demultiplex
nf-core/demultiplex
Demultiplexing pipeline for Illumina sequencing data
Data & utilities44 params1.8.0Pinned Sep 15, 2026
- denovotranscript
nf-core/denovotranscript
A pipeline for de novo transcriptome assembly of short reads from bulk RNA-seq
Transcriptomics52 params1.2.1Pinned Aug 28, 2025
- detaxizer
nf-core/detaxizer
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
Microbial & metagenomics65 params1.4.0Pinned Oct 26, 2026
- differentialabundance
nf-core/differentialabundance
Differential abundance analysis
Transcriptomics188 params2.0.0Pinned Jun 23, 2026
- drop
nf-core/drop
The detection of RNA Outliers Pipeline (DROP) is an integrative workflow to detect aberrant expression, aberrant splicing, and mono-allelic expression from raw sequencing files.
Transcriptomics83 params1.0.0Pinned Apr 2, 2026
- drugresponseeval
nf-core/drugresponseeval
This pipeline evaluates drug response models in various settings on a variety of datasets.
Other41 params1.4.0Pinned Nov 7, 2026
- epitopeprediction
nf-core/epitopeprediction
A fully reproducible and state of the art epitope prediction pipeline.
Proteomics & immunology49 params3.2.0Pinned Oct 15, 2026
- fastqrepair
nf-core/fastqrepair
A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settle reads that became disordered
Data & utilities32 params1.1.1Pinned Aug 31, 2026
- fastquorum
nf-core/fastquorum
fgbio Best Practices FASTQ to Consensus Pipeline
Data & utilities46 params2.0.0Pinned Jun 23, 2026
- fetchngs
nf-core/fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
Data & utilities29 params1.13.0Pinned Sep 15, 2026
- funcprofiler
nf-core/funcprofiler
Read-based functional profiling of microbiome sequencing data
Microbial & metagenomics34 params1.0.0Pinned Sep 21, 2026
- funcscan
nf-core/funcscan
Pipeline for screening for functional components of assembled contigs
Genomes & evolution220 params4.0.0Pinned Jun 27, 2026
- genomeassembler
nf-core/genomeassembler
Assemble genomes from long ONT or pacbio HiFi reads
Genomes & evolution72 params2.0.1Pinned Oct 23, 2026
- genomeqc
nf-core/genomeqc
A pipeline to compare multiple genomes and annotations
Genomes & evolution72 params1.0.1Pinned Sep 16, 2026
- hadge
nf-core/hadge
Comprehensive pipeline for donor demultiplexing in single cell
Single-cell & spatial195 params1.0.0Pinned Sep 28, 2026
- hgtseq
nf-core/hgtseq
A pipeline to investigate horizontal gene transfer from NGS data
Microbial & metagenomics41 params1.1.0Pinned May 16, 2023
- hic
nf-core/hic
Analysis of Chromosome Conformation Capture data (Hi-C)
Epigenomics73 params2.1.0Pinned Jun 1, 2023
- hicar
nf-core/hicar
This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
Epigenomics74 params1.0.0Pinned May 3, 2022
- hlatyping
nf-core/hlatyping
Precision HLA typing from next-generation sequencing data.
Proteomics & immunology36 params2.2.0Pinned Feb 2, 2026
- isoseq
nf-core/isoseq
Genes and transcripts annotation with Isoseq using uLTRA and TAMA
Transcriptomics45 params3.0.1Pinned Sep 23, 2026
- longraredisease
nf-core/longraredisease
A Nextflow pipeline for rare disease diagnostics from Oxford Nanopore long-read sequencing data. Includes SV, SNV, CNV, and methylation profiling.
Variant calling96 params1.0.0Pinned Jun 26, 2026
- lsmquant
nf-core/lsmquant
A pipeline for preprocessing and analysis of large-scale light-sheet microscopy images based on the NuMorph toolbox
Single-cell & spatial29 params1.0.3Pinned Aug 10, 2026
- mag
nf-core/mag
Assembly, binning and annotation of metagenomes
Microbial & metagenomics179 params5.5.0Pinned Aug 1, 2026
- magmap
nf-core/magmap
nf-core/magmap is a bioinformatics best-practice analysis pipeline for mapping reads to (large) collections of genomes.
Genomes & evolution59 params1.3.1Pinned Oct 22, 2026
- marsseq
nf-core/marsseq
MARS-seq v2 preprocessing pipeline
Single-cell & spatial38 params1.0.3Pinned Jul 18, 2023
- mcmicro
nf-core/mcmicro
Whole-slide multiplexed microscopy image analysis
Single-cell & spatial35 params2.0.0Pinned Jul 1, 2026
- metaboigniter
nf-core/metaboigniter
Pre-processing of mass spectrometry-based metabolomics data
Proteomics & immunology229 params2.0.1Pinned Apr 15, 2024
- metapep
nf-core/metapep
From metagenomes to peptides
Microbial & metagenomics38 params1.0.0Pinned Nov 22, 2024
- metatdenovo
nf-core/metatdenovo
Assembly and annotation of metatranscriptomic data, both prokaryotic and eukaryotic
Microbial & metagenomics97 params2.0.0Pinned Oct 7, 2026
- methylong
nf-core/methylong
Extract methylation calls from long reads
Epigenomics49 params2.0.0Pinned Nov 21, 2025
- methylseq
nf-core/methylseq
Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.
Epigenomics88 params4.2.0Pinned Dec 12, 2025
- mhcquant
nf-core/mhcquant
Identify and quantify peptides from mass spectrometry raw data
Proteomics & immunology78 params3.3.0Pinned Oct 2, 2026
- molkart
nf-core/molkart
An analysis pipeline for processing Molecular Cartography data.
Single-cell & spatial62 params1.2.0Pinned Oct 27, 2025
- multiplesequencealign
nf-core/multiplesequencealign
Pipeline to run and benchmark multiple sequence alignment tools.
Genomes & evolution51 params1.1.1Pinned May 27, 2025
- nanoseq
nf-core/nanoseq
A pipeline to demultiplex, QC and map Nanopore data
Data & utilities64 params3.1.0Pinned Mar 10, 2023
- nanostring
nf-core/nanostring
Nanostring nCounter analysis pipeline
Transcriptomics35 params1.3.3Pinned Jan 30, 2026
- nascent
nf-core/nascent
Global Run-On sequencing analysis pipeline
Epigenomics53 params2.3.0Pinned May 7, 2025
- oncoanalyser
nf-core/oncoanalyser
A comprehensive cancer DNA/RNA analysis and reporting pipeline
Variant calling75 params3.0.0Pinned Sep 1, 2026
- pacvar
nf-core/pacvar
A variant caller for PacBio long read sequencing - also can be used for PureTarget panel analysis, and quantification of repeat expansions
Variant calling60 params1.1.0Pinned Jun 24, 2026
- pairgenomealign
nf-core/pairgenomealign
Pairwise alignment pipeline (genome to genome or reads to genome)
Genomes & evolution54 params3.0.4Pinned Aug 26, 2026
- pangenome
nf-core/pangenome
The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs
Genomes & evolution63 params1.1.3Pinned Feb 9, 2025
- pathogensurveillance
nf-core/pathogensurveillance
Surveillance of pathogens using high-throughput sequencing
Microbial & metagenomics53 params1.1.0Pinned Feb 13, 2026
- phaseimpute
nf-core/phaseimpute
Phasing and imputation pipeline
Variant calling58 params1.1.0Pinned Dec 1, 2025
- phyloplace
nf-core/phyloplace
Performs phylogenetic placement with EPA-NG
Genomes & evolution37 params2.3.0Pinned Sep 23, 2026
- pixelator
nf-core/pixelator
Pipeline for analysis of Proximity Network Assay data
Single-cell & spatial84 params6.0.0Pinned Nov 2, 2026
- plasmodiumdrugres
nf-core/plasmodiumdrugres
This pipeline takes PMO format and provides key metrics on supplied markers applicable to drug resistance
Other45 params1.0.0Pinned Oct 9, 2026
- proteinannotator
nf-core/proteinannotator
Generation of sequence-level annotations for amino acid sequences
Proteomics & immunology50 params1.1.0Pinned May 7, 2026
- proteinfamilies
nf-core/proteinfamilies
Generate protein family level models (Multiple Sequence Alignments (MSAs), Hidden Markov Models (HMMs)) starting from a FASTA amino acid sequence file.
Proteomics & immunology68 params2.6.0Pinned Oct 1, 2026
- proteinfold
nf-core/proteinfold
Protein 3D structure prediction pipeline
Proteomics & immunology182 params2.0.0Pinned Mar 27, 2026
- provenancereport
nf-core/provenancereport
Generate reproducible Quarto reports together with an audit trail of inputs, checksums, software versions, runtime environments, and provenance metadata.
Other27 params1.0.1Pinned Nov 10, 2026
- rangeland
nf-core/rangeland
Long-term vegetation trend analysis pipeline for rangeland systems using satellite imagery.
Single-cell & spatial40 params1.0.0Pinned Jan 17, 2025
- raredisease
nf-core/raredisease
call and score variants from WGS/WES of rare disease patients
Variant calling150 params3.1.2Pinned Jul 6, 2026
- readsimulator
nf-core/readsimulator
A workflow to simulate reads
Data & utilities76 params1.0.1Pinned Apr 26, 2024
- reportho
nf-core/reportho
A pipeline for ortholog fetching and analysis
Genomes & evolution51 params1.1.0Pinned Oct 21, 2025
- ribomsqc
nf-core/ribomsqc
QC pipeline that monitors mass spectrometer performance in ribonucleoside analysis
Proteomics & immunology31 paramsv1.0.0Pinned Mar 13, 2026
- riboseq
nf-core/riboseq
Analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting)
Transcriptomics147 params2.0.0Pinned Sep 15, 2026
- rnadnavar
nf-core/rnadnavar
Pipeline for RNA and DNA integrated analysis for somatic mutation detection
Variant calling126 params1.0.0Pinned Jun 29, 2026
- rnafusion
nf-core/rnafusion
Nextflow rnafusion analysis pipeline, part of the nf-core community.
Transcriptomics85 params4.1.3Pinned Jun 2, 2026
- rnaseq
nf-core/rnaseq
RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.
Transcriptomics136 params3.27.0Pinned Sep 23, 2026
- rnasplice
nf-core/rnasplice
Alternative splicing analysis using RNA-seq.
Transcriptomics127 params2.0.0Pinned Oct 20, 2026
- rnastructurome
nf-core/rnastructurome
This pipeline analyses chemical-based high-throughput RNA structure probing data
Transcriptomics190 params1.1.0Pinned Oct 23, 2026
- rnavar
nf-core/rnavar
GATK4 RNA variant calling pipeline
Variant calling106 params1.3.0Pinned Jun 3, 2026
- sarek
nf-core/sarek
An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing
Variant calling182 params3.12.0Pinned Nov 11, 2026
- scnanoseq
nf-core/scnanoseq
Single-cell/nuclei pipeline for data derived from Oxford Nanopore
Single-cell & spatial58 params1.3.0Pinned Jun 26, 2026
- scrnaseq
nf-core/scrnaseq
Pipeline for processing 10x Genomics single cell rnaseq data
Single-cell & spatial69 params4.2.0Pinned Jul 3, 2026
- seqinspector
nf-core/seqinspector
Pipeline to QC your sequences
Data & utilities51 params1.1.2Pinned Aug 19, 2026
- seqsubmit
nf-core/seqsubmit
Submit sequences, assemblies, MAGs, etc., to public archives
Data & utilities39 params1.0.0Pinned Jul 31, 2026
- smrnaseq
nf-core/smrnaseq
Small RNA-Seq Best Practice Analysis Pipeline.
Transcriptomics71 params2.4.1Pinned Jan 7, 2026
- sopa
nf-core/sopa
Technology-invariant pipeline for spatial omics analysis that scales to millions of cells
Single-cell & spatial91 params1.0.2Pinned Nov 3, 2026
- spatialaxe
nf-core/spatialaxe
A pipeline to process spatialomics data from 10x Xenium In Situ or 10x Atera.
Single-cell & spatial103 params1.0.1Pinned Aug 6, 2026
- stableexpression
nf-core/stableexpression
This pipeline is dedicated to identifying the most stable genes within a single or multiple expression dataset(s). This is particularly useful for identifying the most suitable RT-qPCR reference genes for a specific species.
Transcriptomics60 params1.1.0Pinned Oct 7, 2026
- taxprofiler
nf-core/taxprofiler
Taxonomic classification and profiling of shotgun short- and long-read metagenomic data
Microbial & metagenomics133 params2.0.1Pinned Jun 15, 2026
- tumourevo
nf-core/tumourevo
Analysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
Variant calling82 params1.0.0Pinned Oct 1, 2026
- variantbenchmarking
nf-core/variantbenchmarking
Variant Benchmarking pipeline for germline and somatic variant callers
Variant calling60 params1.6.1Pinned Nov 5, 2026
- variantprioritization
nf-core/variantprioritization
pipeline for the functional annotation and translation of somatic SNVs/InDels and copy number abberations for precision cancer medicine
Variant calling111 params1.0.0Pinned Apr 9, 2026
- viralintegration
nf-core/viralintegration
Integration of viral sequences in genomic data
Microbial & metagenomics37 params0.1.1Pinned Jul 19, 2023
- viralmetagenome
nf-core/viralmetagenome
A bioinformatics best-practice analysis pipeline for untargeted viral genome reconstruction and to identify intra-host variants from metagenomic sequencing data.
Microbial & metagenomics196 params1.2.0Pinned Sep 16, 2026
- viralrecon
nf-core/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
Microbial & metagenomics104 params3.0.0Pinned Oct 28, 2025