Pinned Repositories
ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
atacseq
ATAC-seq peak-calling and QC analysis pipeline
chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
mag
Assembly and binning of metagenomes
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
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
A single-cell RNAseq pipeline for 10X genomics data
tools
Python package with helper tools for the nf-core community.
nf-core's Repositories
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/rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
nf-core/eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
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/configs
Config files used to define parameters specific to compute environments at different Institutions
nf-core/raredisease
Call and score variants from WGS/WES of rare disease patients.
nf-core/website
Code and files for the main nf-core website.
nf-core/funcscan
(Meta-)genome screening for functional and natural product gene sequences
nf-core/bacass
Simple bacterial assembly and annotation pipeline
nf-core/differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
nf-core/airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
nf-core/circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
nf-core/demultiplex
Demultiplexing pipeline for sequencing data
nf-core/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`).
nf-core/phaseimpute
nf-core/metatdenovo
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
nf-core/fastquorum
Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
nf-core/variantbenchmarking
A nextflow variant benchmarking pipeline - premature
nf-core/createtaxdb
Parallelised and automated construction of metagenomic classifier databases of different tools
nf-core/rangeland
Pipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.
nf-core/seqinspector
QC pipeline to inspect your sequences
nf-core/callingcards
A pipeline for processing calling cards data
nf-core/reportho
nf-core pipeline for comparative analysis of ortholog predictions
nf-core/magmap
nf-core/references
nf-core/ops