Pinned Repositories
ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
configs
Config files used to define parameters specific to compute environments at different Institutions
mag
Assembly and binning of metagenomes
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
proposals
Where new ideas for nf-core pipelines, special interest groups and more are proposed
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
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
tools
Python package with helper tools for the nf-core community.
nf-core's Repositories
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/chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
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/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
nf-core/test-datasets
Test data to be used for automated testing with the nf-core pipelines
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/oncoanalyser
A comprehensive cancer DNA/RNA analysis and reporting pipeline
nf-core/proteinfold
Protein 3D structure prediction pipeline
nf-core/differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
nf-core/website
Code and files for the main nf-core website.
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/epitopeprediction
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
nf-core/mhcquant
Identify and quantify MHC eluted peptides from mass spectrometry raw data
nf-core/variantbenchmarking
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
nf-core/setup-nextflow
A GitHub action to install Nextflow
nf-core/spatialxe
nf-core/createtaxdb
Parallelised and automated construction of metagenomic classifier databases of different tools
nf-core/metapep
From metagenomes to epitopes and beyond
nf-core/nft-utils
nf-test utility functions
nf-core/drop
Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
nf-core/sammyseq
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
nf-core/ops
Different *Ops related scripts for the nf-core org.
nf-core/nf-core-utils
Nextflow plugin for nf-core utils