nf-core
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155 repositories
tools
Public- Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
- Call and score variants from WGS/WES of rare disease patients.
- Config files used to define parameters specific to compute environments at different Institutions
- Simple bacterial assembly and annotation pipeline
- Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
eager
PublicA fully reproducible and state-of-the-art ancient DNA analysis pipelinedeepmodeloptim
PublicStochastic Testing and Input Manipulation for Unbiased Learning Systemsoncoanalyser
Publicfetchngs
Publicscnanoseq
PublicSingle-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomicscreatetaxdb
PublicParallelised and automated construction of metagenomic classifier databases of different toolsbactmap
Publicmag
PublicAssembly and binning of metagenomessarek
PublicAnalysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing- nf-core/references is a bioinformatics pipeline that build references, for multiple use cases
taxprofiler
PublicHighly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data- Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
- Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
tfactivity
PublicBioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.rnavar
Publicfastquorum
Publicsetup-nextflow
Publicdifferentialabundance
Public