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differentialabundance

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

dualrnaseq

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

eager

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

epitopeprediction

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

exoseq

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

fastquorum

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

fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases

funcscan

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

genomeannotator

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

genomeassembler

genomeskim

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

gh-actions-lint

GitHub Action to run nf-core code linting on a Nextflow pipeline

gwas

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

hgtseq

A pipeline to investigate horizontal gene transfer from NGS data

hic

Analysis of Chromosome Conformation Capture data (Hi-C)

hicar

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

hlatyping

Precision HLA typing from next-generation sequencing data

imcyto

Image Mass Cytometry analysis pipeline

isoseq

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

kmermaid

k-mer similarity analysis pipeline

liverctanalysis

UNDER CONSTRUCTION: pipeline for liver CT analysis

lncpipe

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

logos

Host nf-core logos and templates for making new logos

mag

Assembly and binning of metagenomes

marsseq

MARS-seq v2 pre-processing pipeline with velocity

mcmicro

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

metaboigniter

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

metapep

From metagenomes to epitopes and beyond

metatdenovo

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

methylseq

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