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methylseq

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

mhcquant

Identify and quantify MHC eluted peptides from mass spectrometry raw data

mnaseseq

MNase-seq analysis pipeline using BWA and DANPOS2.

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

molkart

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

multiplesequencealign

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

nanoseq

Nanopore demultiplexing, QC and alignment pipeline

nanostring

An analysis pipeline for Nanostring nCounter expression data.

nascent

Nascent Transcription Processing Pipeline

neutronstar

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

nf-core.github.io

Now replaced with a new website >>>

omicsgenetraitassociation

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

oncoanalyser

A comprehensive cancer DNA/RNA analysis and reporting pipeline

ops

pangenome

Renders a collection of sequences into a pangenome graph.

pathogensurveillance

Surveillance of pathogens using population genomics and sequencing

pgdb

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

phageannotator

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

phaseimpute

phyloplace

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

pixelator

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

prettier-plugin-nextflow

proteinfold

Protein 3D structure prediction pipeline

proteomicslfq

Proteomics label-free quantification (LFQ) analysis pipeline

quantms

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

radseq

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

rangeland

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.

raredisease

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

readsimulator

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

references