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rnaseqRNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
sarekAnalysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
toolsPython package with helper tools for the nf-core community.
modulesRepository to host tool-specific module files for the Nextflow DSL2 community!
magAssembly and binning of metagenomes
chipseqChIP-seq peak-calling, QC and differential analysis pipeline.
atacseqATAC-seq peak-calling, QC and differential analysis pipeline
methylseqMethylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
rnafusionRNA-seq analysis pipeline for detection gene-fusions
ampliseqAmplicon sequencing analysis workflow using DADA2 and QIIME2
nanoseqNanopore demultiplexing, QC and alignment pipeline
eagerA fully reproducible and state-of-the-art ancient DNA analysis pipeline
scrnaseqA single-cell RNAseq pipeline for 10X genomics data
viralreconAssembly and intrahost/low-frequency variant calling for viral samples
taxprofilerHighly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
test-datasetsTest data to be used for automated testing with the nf-core pipelines
configsConfig files used to define parameters specific to compute environments at different Institutions
rarediseaseCall and score variants from WGS/WES of rare disease patients.
hicAnalysis of Chromosome Conformation Capture data (Hi-C)
smrnaseqA small-RNA sequencing analysis pipeline
hlatypingPrecision HLA typing from next-generation sequencing data
bactmapA mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
nf-co.reCode and files for the main nf-core website.
bacassSimple bacterial assembly and annotation pipeline
funcscan(Meta-)genome screening for functional and natural product gene sequences
pangenomeRenders a collection of sequences into a pangenome graph.
circrnacircRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
spatialtranscriptomicsPipeline for processing spatially-resolved gene counts with spatial coordinates, image data, and optionally single cell RNA-seq data, designed for 10x genomics visium and single cell transcriptomics.
proteomicslfqProteomics label-free quantification (LFQ) analysis pipeline
differentialabundanceDifferential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
demultiplexDemultiplexing pipeline for sequencing data
cutandrunAnalysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
mhcquantIdentify and quantify MHC eluted peptides from mass spectrometry raw data
epitopepredictionA bioinformatics best-practice analysis pipeline for epitope prediction and annotation
airrflowB-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
proteinfoldProtein 3D structure prediction pipeline
imcytoImage Mass Cytometry analysis pipeline
cookiecutterDEPRECIATED! Please use nf-core/tools instead
hgtseqA pipeline to investigate horizontal gene transfer from NGS data
quantmsQuantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
kmermaidk-mer similarity analysis pipeline
circdnaPipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
rnavargatk4 RNA variant calling pipeline
clipseqCLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
isoseqGenome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
viprAssembly and intrahost / low-frequency variant calling for viral samples
dualrnaseqAnalysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
gwasUNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies
exoseqPlease consider using/contributing to https://github.com/nf-core/sarek
diaproteomicsAutomated quantitative analysis of DIA proteomics mass spectrometry measurements.
rnasplicernasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
mnaseseqMNase-seq analysis pipeline using BWA and DANPOS2.
nascentNascent Transcription Processing Pipeline
vscode-extensionpackA VSCode extension pack for nf-core developers.
cageseqCAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
bamtofastqConverts bam or cram files to fastq format and does quality control.
genomeannotatorPipeline for the identification of (coding) gene structures in draft genomes.
fastquorumPipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
crisprseqA pipeline for the analysis of CRISPR edited next generation sequencing (NGS) data. CRISPR gene knockouts (KO), CRISPR knock-ins (KI), base editing (BE) and prime editing (PE) experiments
coproidCoprolite host Identification pipeline
multiplesequencealignA pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
metapepFrom metagenomes to epitopes and beyond
nf-core.github.ioNow replaced with a new website >>>
awsmegatestsCloudFormation templates to setup the aws megatests necessary cloud infrastructure
crisprvar[WIP] Evaluate outcomes from genome editing experiments
hicarPipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
gh-actions-lintGitHub Action to run nf-core code linting on a Nextflow pipeline
nanostringAn analysis pipeline for Nanostring nCounter expression data.
neutronstarDe novo assembly pipeline for 10X linked-reads using Supernova
marsseqMARS-seq v2 pre-processing pipeline with velocity
metatdenovoAssembly and annotation of metatranscriptomic data, both prokaryotic and eukaryotic.
phyloplacenf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
logosHost nf-core logos and templates for making new logos
actions-runnersInstructions and scripts for custom GitHub Actions runners
testpipelineA small example pipeline used to test new nf-core infrastructure and common code.
callingcardsA pipeline for processing calling cards data
pixelatorNextflow nf-core pipeline to generate Molecular Pixelation data with pixelator (Pixelgen Technologies AB)
ssdsSingle-stranded DNA Sequencing (SSDS) nf-core pipeline