nf-core

rnaseq

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

sarek

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

modules

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

tools

Python package with helper tools for the nf-core community.

mag

Assembly and binning of metagenomes

rnafusion

RNA-seq analysis pipeline for detection of gene-fusions

fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases

viralrecon

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

taxprofiler

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

test-datasets

Test data to be used for automated testing with the nf-core pipelines

configs

Config files used to define parameters specific to compute environments at different Institutions

website

Code and files for the main nf-core website.

funcscan

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

bacass

Simple bacterial assembly and annotation pipeline

proteinfold

Protein 3D structure prediction pipeline

circrna

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

rnavar

gatk4 RNA variant calling pipeline

scflow

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

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`).

oncoanalyser

A comprehensive cancer DNA/RNA analysis and reporting pipeline

phaseimpute

setup-nextflow

A GitHub action to install Nextflow

molkart

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

tfactivity

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

reportho

nf-core pipeline for comparative analysis of ortholog predictions

variantbenchmarking

A nextflow variant benchmarking pipeline - premature

createpanelrefs

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

scdownstream

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

magmap

ops