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/hic
Analysis of Chromosome Conformation Capture data (Hi-C)
nf-core/proteomicslfq
Proteomics label-free quantification (LFQ) analysis pipeline
nf-core/quantms
Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
nf-core/genomeannotator
Pipeline for the identification of (coding) gene structures in draft genomes.
nf-core/circdna
Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
nf-core/scflow
Please consider using/contributing to https://github.com/nf-core/scdownstream
nf-core/detaxizer
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
nf-core/kmermaid
k-mer similarity analysis pipeline
nf-core/diaproteomics
Automated quantitative analysis of DIA proteomics mass spectrometry measurements.
nf-core/viralintegration
Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.
nf-core/tower-action
GitHub Action to launch a workflow using Nextflow Tower.
nf-core/mnaseseq
MNase-seq analysis pipeline using BWA and DANPOS2.
nf-core/omicsgenetraitassociation
A nextflow pipeline which integrates multiple omic data streams and performs coordinated analysis
nf-core/denovohybrid
UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads
nf-core/slamseq
SLAMSeq processing and analysis pipeline
nf-core/marsseq
MARS-seq v2 pre-processing pipeline with velocity
nf-core/pgdb
The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.
nf-core/sublime
Nextflow workflow syntax highlighting and snippets for Sublime Text 4
nf-core/prettier-plugin-nextflow
nf-core/crisprvar
[WIP] Evaluate outcomes from genome editing experiments
nf-core/gh-actions-lint
GitHub Action to run nf-core code linting on a Nextflow pipeline
nf-core/ddamsproteomics
Quantitative shotgun MS proteomics
nf-core/modules-template
nf-core/genomeskim
QC and filtering of genome skims, followed by organelle assembly and/or genome analysis
nf-core/.github
Files for the @nf-core GitHub organisation
nf-core/basic_training
Hosts the content of the basic nf-core training on how to create nf-core pipelines with `nf-core create`
nf-core/hackathon
All about the nf-core hackathons
nf-core/ssds
Single-stranded DNA Sequencing (SSDS) nf-core pipeline
nf-core/vale
Spelling and grammar linting for nf-core documentation
nf-core/liverctanalysis
UNDER CONSTRUCTION: pipeline for liver CT analysis