Pipelines
Browse the 133 pipelines that are currently available as part of nf-core.
Parallelised and automated construction of metagenomic classifier databases of different tools
1.0.0 released 4 days ago
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
1.2.0 released 5 days ago
Converts bam or cram files to fastq format and does quality control.
2.2.0 released 6 days ago
Generation and update of protein families
1.2.0 released 7 days ago
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
4.3.1 released 13 days ago
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
1.2.0 released 13 days ago
A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
1.1.1 released 26 days ago
Identify and quantify MHC eluted peptides from mass spectrometry raw data
3.0.0 released about 1 month ago
Assembly and binning of metagenomes
4.0.0 released about 1 month ago
Call and score variants from WGS/WES of rare disease patients.
2.5.0 released about 1 month ago
Coprolite host Identification pipeline
2.0.0 released about 1 month ago
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
2.1.0 released about 1 month ago
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
3.0.0 released about 1 month ago
Demultiplexing pipeline for sequencing data
1.6.1 released about 2 months ago
Precision HLA typing from next-generation sequencing data
2.1.0 released 2 months ago
Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
1.2.0 released 2 months ago
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
1.2.0 released 3 months ago
Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
1.0.1 released 3 months ago
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
2.5.3 released 3 months ago
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
1.2.3 released 3 months ago
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
4.0.0 released 3 months ago
Longread PacBio sequencing processing for WGS and PureTarget
1.0.1 released 4 months ago
A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
1.1.0 released 4 months ago
(Meta-)genome screening for functional and natural product gene sequences
2.1.0 released 4 months ago
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
2.0.0 released 4 months ago
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
3.5.1 released 4 months ago
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
1.1.3 released 4 months ago
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
1.0.0 released 5 months ago
Pipeline for testing drug response prediction models in a statistically and biologically sound way.
1.0.0 released 5 months ago
A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq
1.2.0 released 5 months ago
An analysis pipeline for Nanostring nCounter expression data.
1.3.1 released 5 months ago
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
1.4.0 released 5 months ago
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.
1.0.0 released 5 months ago
nf-core/references is a bioinformatics pipeline that build references, for multiple use cases
0.1 released 6 months ago
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
3.0.0 released 6 months ago
A bioinformatics pipeline to phase and impute genetic data
1.0.0 released 7 months ago
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
1.1.0 released 8 months ago
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
).
2.3.0 released 8 months ago
ChIP-seq peak-calling, QC and differential analysis pipeline.
2.1.0 released 9 months ago
Protein 3D structure prediction pipeline
1.1.1 released 11 months ago
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
1.5.0 released about 1 year ago
A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.
1.0.1 released about 1 year ago
Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.
2.0.1 released about 1 year ago
RNA-seq analysis pipeline for detection of gene-fusions
3.0.2 released about 1 year ago
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.
1.1.0 released over 1 year ago
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
3.2.2 released over 1 year ago
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
1.2.0 released over 1 year ago
ATAC-seq peak-calling and QC analysis pipeline
2.1.2 released almost 2 years ago
Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.
0.1.1 released almost 2 years ago
MARS-seq v2 pre-processing pipeline with velocity
1.0.3 released almost 2 years ago
Analysis of Chromosome Conformation Capture data (Hi-C)
2.1.0 released about 2 years ago
Assembly and intrahost/low-frequency variant calling for viral samples
2.6.0 released about 2 years ago
MNase-seq analysis pipeline using BWA and DANPOS2.
1.0.0 released about 3 years ago
Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
1.0.0 released about 3 years ago
Automated quantitative analysis of DIA proteomics mass spectrometry measurements.
1.2.4 released about 4 years ago
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
1.0.0 released about 4 years ago
The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.
1.0.0 released about 4 years ago
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
1.0.0 released over 4 years ago
CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
1.0.2 released over 4 years ago
k-mer similarity analysis pipeline
0.1.0-alpha released over 4 years ago
Proteomics label-free quantification (LFQ) analysis pipeline
1.0.0 released over 4 years ago
Image Mass Cytometry analysis pipeline
1.0.0 released about 5 years ago
SLAMSeq processing and analysis pipeline
1.0.0 released about 5 years ago
De novo assembly pipeline for 10X linked-reads using Supernova
1.0.0 released over 5 years ago
Please consider using/contributing to https://github.com/nf-core/sarek
1.0 released over 6 years ago
last changes about 1 month ago
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
last changes about 1 month ago
Generate Panel of Normals, models or other similar references from lots of samples
last changes 5 days ago
Stochastic Testing and Input Manipulation for Unbiased Learning Systems
last changes 7 days ago
A pipeline for network-based disease module identification.
last changes about 1 month ago
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)
last changes 13 days ago
Pipeline for the identification of (coding) gene structures in draft genomes.
last changes about 3 years ago
Compare the quality of multiple genomes, along with their annotations.
last changes 2 months ago
QC and filtering of genome skims, followed by organelle assembly and/or genome analysis
last changes almost 3 years ago
UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
last changes 3 months ago
A pipeline for processing and analysis of light-sheet microscopy images.
last changes about 1 month ago
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
last changes 5 days ago
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.
last changes about 1 month ago
A-Z analysis of mitochondrial NGS data
last changes 4 months ago
A nextflow pipeline which integrates multiple omic data streams and performs coordinated analysis
last changes over 1 year ago
Surveillance of pathogens using population genomics and sequencing
last changes 5 days ago
Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.
last changes about 1 year ago
The best protein annotation pipeline in the world. Protein fasta → ??? → Annotations
last changes 19 days ago
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
last changes 12 days ago
A single cell transcriptomics pipeline for QC, integration and making the data presentable
last changes about 15 hours ago
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
last changes 11 days ago
Pipeline for simulating the first industrial revolution using Agent Based Models.
last changes about 1 year ago
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.
last changes about 1 month ago
An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.
last changes 8 months ago
Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
last changes 4 days ago
A quantitative assessment of the underlying permafrost landscapes and, per extension, of the level of permafrost thaw in the region
last changes 5 months ago
Analysis pipleine to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
last changes 5 months ago
Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.
last changes about 2 years ago
Assembly and intrahost / low-frequency variant calling for viral samples
last changes over 6 years ago
Single-stranded DNA Sequencing (SSDS) nf-core pipeline
last changes over 3 years ago
Please consider using/contributing to https://github.com/nf-core/scdownstream
last changes about 1 year ago
UNDER CONSTRUCTION: pipeline for liver CT analysis
last changes almost 4 years ago
Please consider using/contributing to https://github.com/nf-core/sarek
last changes over 6 years ago
UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads
last changes almost 6 years ago