nf-core
There are 167 repositories under nf-core topic.
nf-core/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
nf-core/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
nf-core/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
nf-core/tools
Python package with helper tools for the nf-core community.
nf-core/mag
Assembly and binning of metagenomes
nf-core/scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
nf-core/chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
nf-core/atacseq
ATAC-seq peak-calling and QC analysis pipeline
nf-core/nanoseq
Nanopore demultiplexing, QC and alignment pipeline
nf-core/fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
nf-core/eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
nf-core/rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
nf-core/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
nf-core/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
nf-core/test-datasets
Test data to be used for automated testing with the nf-core pipelines
nf-core/hic
Analysis of Chromosome Conformation Capture data (Hi-C)
nf-core/raredisease
Call and score variants from WGS/WES of rare disease patients.
nf-core/configs
Config files used to define parameters specific to compute environments at different Institutions
nf-core/cutandrun
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
nf-core/pangenome
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
nf-core/funcscan
(Meta-)genome screening for functional and natural product gene sequences
nf-core/smrnaseq
A small-RNA sequencing analysis pipeline
nf-core/website
Code and files for the main nf-core website.
nf-core/differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
nf-core/bacass
Simple bacterial assembly and annotation pipeline
nf-core/hlatyping
Precision HLA typing from next-generation sequencing data
nf-core/proteinfold
Protein 3D structure prediction pipeline
nf-core/airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
nf-core/bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
nf-core/spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
nf-core/oncoanalyser
A comprehensive cancer DNA/RNA analysis and reporting pipeline
nf-core/rnasplice
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
nf-core/circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
nf-core/demultiplex
Demultiplexing pipeline for sequencing data