AliNe
AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignment - Published in JOSS (2025)
nf-gwas-pipeline
nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline - Published in JOSS (2021)
ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis
ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - Published in JOSS (2022)
dockstore
An app store for scientific workflows, tools, notebooks, and services
scrnaseq
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
cutandrun
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
clipseq
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
dualrnaseq
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
funcscan
(Meta-)genome screening for functional and natural product gene sequences
epitopeprediction
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
pipelines-nextflow
A set of workflows written in Nextflow for Genome Annotation.
crisprseq
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`).
bamtofastq
Converts bam or cram files to fastq format and does quality control.
mcmicro
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
circdna
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.
genomeassembler
Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
euryale
A pipeline for taxonomic classification and functional annotation of metagenomic reads. Based on MEDUSA
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.
nextits
A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio
cnr-flow
CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.
taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
configs
Config files used to define parameters specific to compute environments at different Institutions
fastquorum
Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
metatdenovo
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
test-datasets
Test data to be used for automated testing with the nf-core pipelines
molkart
A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
phyloplace
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
viralintegration
Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.
bpertussis-ciwgs
Culture-Independent Whole Genome Sequencing (CIWGS) Read Filter Pipeline 🧪🧬🖥️
variantcatalogue
Pipeline to generate variant catalogues, a list of variants and their frequencies in a population, from whole genome sequences.
metaboigniter
Pre-processing of mass spectrometry-based metabolomics data with quantification and identification based on MS1 and MS2 data.
genomeannotator
Pipeline for the identification of (coding) gene structures in draft genomes.
cronology
cronology is an automated workflow for Cronobacter whole genome sequence assembly, subtyping and isolate clustering based on NCBI Pathogen Detection Project for Cronobacter.
https://github.com/agahkarakuzu/bids2nf
Emits nextflow channels from Brain Imaging Data Structure data.
bacannot
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
pixelator
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
what_the_phage
WtP: Phage identification via nextflow and docker or singularity
evexplorer
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)
variantbenchmarking
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
panoramaseq
a pipeline to process sequencing based spatial transccriptomics data from in-situ arrays
scdownstream
A single cell transcriptomics pipeline for QC, integration and making the data presentable
aradeepopsis
A versatile, fully open-source pipeline to extract phenotypic measurements from plant images
https://github.com/cidgoh/nf-ncov-voc
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 or Mpox genomes. Workflow is developed in collaboration with VIRUS-MVP (https://github.com/cidgoh/VIRUS-MVP) which can be used to visualize the mutation profiles and functional annotations.