Scientific software, databases and pipelines — run for you.

Software

Bioinformatics programs the research agent runs on its own machine — preinstalled, or set up the first time a task needs them.

Databases

Scientific databases the agent searches directly — no account, no API key — with the source record linked from every answer.

Pipelines

Every nf-core pipeline, run with Nextflow on the agent's machine — or handed to you as a validated command for your own cluster.

• nf-core/abotyperA pipeline for characterising the Human Blood Group and Red Cell Antigens using Oxford Nanopore third-generation sequencing data.
• nf-core/airrflowB-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
• nf-core/alleleexpressionAlleleexpression is a nf-core pipeline for allele-specific expression (ASE) analysis using STAR-WASP for alignment, UMI-tools for deduplication, and phaser for haplotype phasing and ASE detection.
• nf-core/ampliseqAmplicon sequencing analysis workflow using DADA2 and QIIME2
• nf-core/atacseqATAC-seq peak-calling and QC analysis pipeline
• nf-core/bacassSimple bacterial assembly and annotation pipeline
• nf-core/bacmodelSystems-based bacterial functional modeling pipeline
• nf-core/bactmapA mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
• nf-core/bamtofastqConverts bam or cram files to fastq format and does quality control.
• nf-core/cageseqCAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
• nf-core/callingcardsA pipeline for processing calling cards data
• nf-core/cellpainting
• nf-core/chipseqChIP-seq peak-calling, QC and differential analysis pipeline.
• nf-core/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.
• nf-core/circrnacircRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
• nf-core/clipseqCLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
• nf-core/coproidCoprolite host Identification pipeline
• nf-core/createpanelrefsGenerate Panel of Normals, models or other similar references from lots of samples
• nf-core/createtaxdbParallelised and automated construction of metagenomic classifier databases of different tools
• nf-core/crisprseqA pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
• nf-core/cutandrunAnalysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
• nf-core/daamicrobiomeMicrobiome differential abundance consensus pipeline
• nf-core/dartseqPipeline for m6A detection in RNAseq data
• nf-core/datasyncnf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks
• nf-core/deepmodeloptimStochastic Testing and Input Manipulation for Unbiased Learning Systems
• nf-core/deepmutscannf-core/deepmutscan is a reproducible, scalable, and community-curated pipeline for analyzing deep mutational scanning (DMS) data using shotgun DNA sequencing.
• nf-core/demonf-core/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.
• nf-core/demultiplexDemultiplexing pipeline for sequencing data
• nf-core/denovotranscriptA pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq
• nf-core/detaxizerA pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
• nf-core/diaproteomicsAutomated quantitative analysis of DIA proteomics mass spectrometry measurements.
• nf-core/differentialabundanceDifferential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
• nf-core/diseasemodulediscoveryA pipeline for network-based disease module identification.
• nf-core/dropPipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
• nf-core/drugresponseevalPipeline for testing drug response prediction models in a statistically and biologically sound way.
• nf-core/dualrnaseqAnalysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
• nf-core/eagerA fully reproducible and state-of-the-art ancient DNA analysis pipeline
• nf-core/epigenomesegmentationAn nf-core pipeline for epigenome segmentation using EpiSegMix/Meth — a hidden Markov model with flexible read count distributions and state duration modeling for histone, open chromatin, and methylation signals.
• nf-core/epitopepredictionA bioinformatics best-practice analysis pipeline for epitope prediction and annotation
• nf-core/evexplorernf-core/evexplorer is a pipeline for analyzing RNA data from extracellular vesicles, compatible with technologies such as nextflex, comboSeq, and ONT with further support forthcoming. evexplorer handles QC, expressed region detection, library size normalization and Differential RNA Expression (DRE)
• nf-core/fastqrepairA pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered
• nf-core/fastquorumPipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
• nf-core/fetchngsPipeline to fetch metadata and raw FastQ files from public databases
• nf-core/funcprofilerRead-based functional profiling of microbiome sequencing data
• nf-core/funcscan(Meta-)genome screening for functional and natural product gene sequences
• nf-core/genephylomodelerA bioinformatics pipeline that fits evolutionary models and detects natural selection from multiple sequence alignments
• nf-core/genomeannotatorPipeline for the identification of (coding) gene structures in draft genomes.
• nf-core/genomeassemblerAssembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
• nf-core/genomeqcCompare the quality of multiple genomes, along with their annotations.
• nf-core/genomeskimQC and filtering of genome skims, followed by organelle assembly and/or genome analysis
• nf-core/genomicrelatednessBioinformatics pipeline for estimating genetic relatedness from low-coverage whole-genome sequencing (sWGS) data
• nf-core/gwasUNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies
• nf-core/hadgeComprehensive pipeline for donor demultiplexing in single cell
• nf-core/hgtseqA pipeline to investigate horizontal gene transfer from NGS data
• nf-core/hicAnalysis of Chromosome Conformation Capture data (Hi-C)
• nf-core/hicarPipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
• nf-core/hlatypingPrecision HLA typing from next-generation sequencing data
• nf-core/imcytoImage Mass Cytometry analysis pipeline
• nf-core/isoseqGenome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
• nf-core/kmermaidk-mer similarity analysis pipeline
• nf-core/lncpipeUNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
• nf-core/longrarediseaseLong read sequencing pipeline to identify variants in patients with neurodevelopmental disorders
• nf-core/lsmquantA pipeline for processing and analysis of light-sheet microscopy images.
• nf-core/magAssembly and binning of metagenomes
• nf-core/magmapBest-practice analysis pipeline for mapping reads to a (large) collections of genomes
• nf-core/marsseqMARS-seq v2 pre-processing pipeline with velocity
• nf-core/mcmicroAn end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
• nf-core/meerpipenf-core/meerpipe is a astronomy pipeline that processes MeerKAT pulsar data to produce images and data products for pulsar timing analysis
• nf-core/metaboigniterPre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.
• nf-core/metapepFrom metagenomes to epitopes and beyond
• nf-core/metatdenovoAssembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
• nf-core/methylarrayProcess methylation data from Illumina arrays. Pre-processing, quality checks, confounder check and DMPs (differentially methylated positions) and DMRs (differentially methylated regions). Optionally estimates cell type composition and adjusts data for it.
• nf-core/methylongExtract methylation calls from long reads (ONT/ PacBio)
• nf-core/methylseqMethylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
• nf-core/mhcquantIdentify and quantify MHC eluted peptides from mass spectrometry raw data
• nf-core/mitodetectA-Z analysis of mitochondrial NGS data
• nf-core/mnaseseqMNase-seq analysis pipeline using BWA and DANPOS2.
• nf-core/molkartA pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
• nf-core/mspepidThis pipeline performs the peptide identification of MS2 spectra from a proteomics experiment. For this, different search algorithm and rescoring approaches can be selected.
• nf-core/multiplesequencealignA pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
• nf-core/nanoseqNanopore demultiplexing, QC and alignment pipeline
• nf-core/nanostringAn analysis pipeline for Nanostring nCounter expression data.
• nf-core/nascentNascent Transcription Processing Pipeline
• nf-core/ncrnannotatornf-core pipeline for genome-level ncRNA annotation using Infernal
• nf-core/omicsgenetraitassociationA nextflow pipeline which integrates multiple omic data streams and performs coordinated analysis
• nf-core/oncoanalyserA comprehensive cancer DNA/RNA analysis and reporting pipeline
• nf-core/pacsomaticNextflow pipeline for PacBio HiFi tumor/normal somatic genomics
• nf-core/pacvarLongread PacBio sequencing processing for WGS and PureTarget
• nf-core/pairgenomealignPairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
• nf-core/pangenomeRenders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
• nf-core/panoramaseqa pipeline to process sequencing based spatial transccriptomics data from in-situ arrays
• nf-core/pathogenepidemiology[UNDER DEVELOPMENT] A profile-based pipeline for genomic epidemiological analysis of predefined pathogens.
• nf-core/pathogensurveillanceSurveillance of pathogens using population genomics and sequencing
• nf-core/phageannotatorPipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.
• nf-core/phaseimputeA bioinformatics pipeline to phase and impute genetic data
• nf-core/phyloplacenf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
• nf-core/pixelatorPipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)
• nf-core/plasmodiumdrugresPipeline for analyzing drug resistance markers from Plasmodium microhaplotype data. It translates variants into amino acid changes at drug resistance loci and estimates allele frequencies and prevalences at both single-locus and multi-locus levels. Microhaplotype data can be supplied in the form of an allele table or a PMO file.
• nf-core/proteinannotatorGeneration of sequence-level annotations for amino acid sequences
• nf-core/proteinfamiliesGeneration and updating of protein families
• nf-core/proteinfoldProtein 3D structure prediction pipeline
• nf-core/proteogenomicsdbThe ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.
• nf-core/provenancereportA simple provenance reporting pipeline
• nf-core/radseqVariant-calling pipeline for Restriction site-associated DNA sequencing (RADseq).
• nf-core/rangelandPipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.
• nf-core/rarediseaseCall and score variants from WGS/WES of rare disease patients.
• nf-core/rarevariantburdenPipeline for performing consistent summary count based rare variant burden test, which is useful when we only have sequenced cases data. For example, we can compare the cases against public summary count data, such as gnomAD.
• nf-core/readsimulatorA pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.
• nf-core/referencesnf-core/references is a bioinformatics pipeline that build references, for multiple use cases
• nf-core/reporthonf-core pipeline for comparative analysis of ortholog predictions
• nf-core/ribomsqcQC pipeline that monitors mass spectrometer performance in ribonucleoside analysis
• nf-core/riboseqPipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
• nf-core/rnadnavarPipeline for RNA and DNA integrated analysis for somatic mutation detection
• nf-core/rnafusionRNA-seq analysis pipeline for detection of gene-fusions
• nf-core/rnaseqRNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
• nf-core/rnasplicernasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
• nf-core/rnastructuromea bioinformatics pipeline for analysing chemical high-throughput RNA structure-probing data
• nf-core/rnavargatk4 RNA variant calling pipeline
• nf-core/sammyseqPipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
• nf-core/sarekAnalysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
• nf-core/scdownstreamA single cell transcriptomics pipeline for QC, integration and making the data presentable
• nf-core/scnanoseqSingle-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
• nf-core/scrnaseqSingle-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
• nf-core/seqinspectorDedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.
• nf-core/seqsubmitnf-core pipeline for data submission to ENA
• nf-core/slamseqSLAMSeq processing and analysis pipeline
• nf-core/smrnaseqA small-RNA sequencing analysis pipeline
• nf-core/sopaNextflow version of Sopa - spatial omics pipeline and analysis
• nf-core/spatialaxeA bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data
• nf-core/spatialviPipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
• nf-core/spinningjennyPipeline for simulating the first industrial revolution using Agent Based Models.
• nf-core/stableexpressionThis 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.
• nf-core/taxprofilerHighly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
• nf-core/tbanalyzerAn nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.
• nf-core/tfactivityBioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
• nf-core/troughgraphA quantitative assessment of the underlying permafrost landscapes and, per extension, of the level of permafrost thaw in the region
• nf-core/tumourevoAnalysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
• nf-core/variantbenchmarkingPipeline to evaluate and validate the accuracy of variant calling methods in genomic research
• nf-core/variantcataloguePipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.
• nf-core/variantprioritizationBioinformatics analysis pipeline for the functional annotation and translation of somatic SNVs/InDels and copy number abberations for precision cancer medicine using Personal Cancer Genome Reporter (PCGR). The pipeline offers germline SNVs/INDELS intepretation and annotation using Cancer Predisposition Sequencing Reporter (CPSR).
• nf-core/viralintegrationAnalysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.
• nf-core/viralmetagenomeA nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
• nf-core/viralreconAssembly and intrahost/low-frequency variant calling for viral samples
• nf-core/crisprvararchived[WIP] Evaluate outcomes from genome editing experiments
• nf-core/ddamsproteomicsarchivedQuantitative shotgun MS proteomics
• nf-core/deepvariantarchivedPlease consider using/contributing to https://github.com/nf-core/sarek
• nf-core/denovohybridarchivedUNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads
• nf-core/exoseqarchivedPlease consider using/contributing to https://github.com/nf-core/sarek
• nf-core/liverctanalysisarchivedUNDER CONSTRUCTION: pipeline for liver CT analysis
• nf-core/neutronstararchivedDe novo assembly pipeline for 10X linked-reads using Supernova
• nf-core/proteomicslfqarchivedProteomics label-free quantification (LFQ) analysis pipeline
• nf-core/quantmsarchivedQuantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
• nf-core/scflowarchivedPlease consider using/contributing to https://github.com/nf-core/scdownstream
• nf-core/smartseq2archivedA pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.
• nf-core/ssdsarchivedSingle-stranded DNA Sequencing (SSDS) nf-core pipeline
• nf-core/viprarchivedAssembly and intrahost / low-frequency variant calling for viral samples