nf-core

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

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

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

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

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

Assembly and binning of metagenomes

Amplicon sequencing analysis workflow using DADA2 and QIIME2

ChIP-seq peak-calling, QC and differential analysis pipeline.

ATAC-seq peak-calling and QC analysis pipeline

Nanopore demultiplexing, QC and alignment pipeline

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

Pipeline to fetch metadata and raw FastQ files from public databases

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

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

RNA-seq analysis pipeline for detection of gene-fusions

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

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

A comprehensive cancer DNA/RNA analysis and reporting pipeline

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

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

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

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

Protein 3D structure prediction pipeline

Analysis of Chromosome Conformation Capture data (Hi-C)

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

Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.

A small-RNA sequencing analysis pipeline

Code and files for the main nf-core website.

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

Simple bacterial assembly and annotation pipeline

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

Precision HLA typing from next-generation sequencing data

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

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...

gatk4 RNA variant calling pipeline

Surveillance of pathogens using population genomics and sequencing

Demultiplexing pipeline for sequencing data

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

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics

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

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

Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research

Identify and quantify MHC eluted peptides from mass spectrometry raw data