Pipelines

A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.

Converts bam or cram files to fastq format and does quality control.

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Identify and quantify MHC eluted peptides from mass spectrometry raw data

Assembly and binning of metagenomes

Call and score variants from WGS/WES of rare disease patients.

Coprolite host Identification pipeline

Generation and update of protein families

Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results

A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

Extract methylation calls from long reads (ONT/ PacBio)

Nascent Transcription Processing Pipeline

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

Demultiplexing pipeline for sequencing data

Precision HLA typing from next-generation sequencing data

Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)

A comprehensive cancer DNA/RNA analysis and reporting pipeline

gatk4 RNA variant calling pipeline

Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research

Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

Longread PacBio sequencing processing for WGS and PureTarget

A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)

(Meta-)genome screening for functional and natural product gene sequences

nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.

A 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

Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.

Pipeline for testing drug response prediction models in a statistically and biologically sound way.

A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq

An analysis pipeline for Nanostring nCounter expression data.

Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)

Pipeline 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/references is a bioinformatics pipeline that build references, for multiple use cases

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

A bioinformatics pipeline to phase and impute genetic data

From metagenomes to epitopes and beyond

Simple bacterial assembly and annotation pipeline

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.

A 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/demo is a simple nf-core style bioinformatics pipeline for workshops and demos.

A small-RNA sequencing analysis pipeline

ChIP-seq peak-calling, QC and differential analysis pipeline.

Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

Protein 3D structure prediction pipeline

nf-core pipeline for comparative analysis of ortholog predictions

A pipeline for processing calling cards data

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.

Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.

RNA-seq analysis pipeline for detection of gene-fusions

Pipeline to fetch metadata and raw FastQ files from public databases

Pipeline 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.

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

ATAC-seq peak-calling and QC analysis pipeline

Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.

MARS-seq v2 pre-processing pipeline with velocity

Analysis of Chromosome Conformation Capture data (Hi-C)

A pipeline to investigate horizontal gene transfer from NGS data

Assembly and intrahost/low-frequency variant calling for viral samples

Nanopore demultiplexing, QC and alignment pipeline

MNase-seq analysis pipeline using BWA and DANPOS2.

Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.

The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.

Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

k-mer similarity analysis pipeline

Proteomics label-free quantification (LFQ) analysis pipeline

Image Mass Cytometry analysis pipeline

SLAMSeq processing and analysis pipeline

De novo assembly pipeline for 10X linked-reads using Supernova

Please consider using/contributing to https://github.com/nf-core/sarek

A pipeline for characterising the Human Blood Group and Red Cell Antigens using Oxford Nanopore third-generation sequencing data.

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

Generate Panel of Normals, models or other similar references from lots of samples

Parallelised and automated construction of metagenomic classifier databases of different tools

nf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks

Stochastic Testing and Input Manipulation for Unbiased Learning Systems

A pipeline for network-based disease module identification.

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

nf-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)

Pipeline for the identification of (coding) gene structures in draft genomes.

Compare the quality of multiple genomes, along with their annotations.

QC and filtering of genome skims, followed by organelle assembly and/or genome analysis

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

A pipeline for processing and analysis of light-sheet microscopy images.

Best-practice analysis pipeline for mapping reads to a (large) collections of genomes

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

nf-core/meerpipe is a astronomy pipeline that processes MeerKAT pulsar data to produce images and data products for pulsar timing analysis

Process 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.

A-Z analysis of mitochondrial NGS data

A nextflow pipeline which integrates multiple omic data streams and performs coordinated analysis

Surveillance of pathogens using population genomics and sequencing

Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.

The best protein annotation pipeline in the world. Protein fasta → ??? → Annotations

Variant-calling pipeline for Restriction site-associated DNA sequencing (RADseq).

QC pipeline that monitors mass spectrometer performance in ribonucleoside analysis

Pipeline for RNA and DNA integrated analysis for somatic mutation detection

Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.

A single cell transcriptomics pipeline for QC, integration and making the data presentable

QC pipeline to inspect your sequences

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Pipeline for simulating the first industrial revolution using Agent Based Models.

Pipeline dedicated to finding the most stable genes among a single or multiple expression dataset(s). It is useful in particular for finding the most suitable RT-qPCR reference genes for a specific species.

An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.

Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

A quantitative assessment of the underlying permafrost landscapes and, per extension, of the level of permafrost thaw in the region

Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)

Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.

Assembly and intrahost / low-frequency variant calling for viral samples

Single-stranded DNA Sequencing (SSDS) nf-core pipeline

A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.

Please consider using/contributing to https://github.com/nf-core/scdownstream

UNDER CONSTRUCTION: pipeline for liver CT analysis

Please consider using/contributing to https://github.com/nf-core/sarek

UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads

Quantitative shotgun MS proteomics

[WIP] Evaluate outcomes from genome editing experiments