nf-core

There are 4 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 nextflow workflow rna-seq rna pipeline
Language:Nextflow 789
nf-core / sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
nextflow workflow pipeline bioinformatics genomics cancer next-generation-sequencing conda reproducible-research containers germline somatic variant-calling nf-core gatk4 annotation whole-genome-sequencing whole-exome-sequencing pre-processing target-panels
Language:Nextflow 340
nf-core / modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
nf-core nextflow modules workflows pipelines dsl2 nf-test
Language:Nextflow 257
nf-core / tools
Python package with helper tools for the nf-core community.
bioinformatics linter linting nextflow nf-core pipeline python workflow
Language:Python 217
nf-core / mag
Assembly and binning of metagenomes
workflow nextflow metagenomics assembly binning annotation nf-core pipeline bioinformatics nanopore nanopore-sequencing metagenomes long-read-sequencing
Language:Nextflow 182
nf-core / chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
nf-core nextflow workflow chip-seq chromatin-immunoprecipitation peak-calling chip pipeline macs2
Language:Nextflow 172
nf-core / scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
nf-core nextflow workflow pipeline 10x-genomics 10xgenomics alevin bustools cellranger kallisto rna-seq single-cell star-solo
Language:Nextflow 169
nf-core / atacseq
ATAC-seq peak-calling and QC analysis pipeline
nf-core nextflow workflow atac-seq chromatin-accessibiity pipeline
Language:Nextflow 161
nf-core / ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
amplicon-sequencing 16s nf-core nextflow pipeline workflow metagenomics rrna 18s its metabarcoding qiime2 edna taxonomic-classification illumina iontorrent microbiome pacbio taxonomic-profiling
Language:Nextflow 157
nf-core / nanoseq
Nanopore demultiplexing, QC and alignment pipeline
alignment demultiplexing nanopore nextflow nf-core pipeline qc workflow
Language:Nextflow 144
nf-core / methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
nf-core nextflow workflow bisulfite-sequencing dna-methylation methyl-seq pipeline em-seq epigenome epigenomics pbat rrbs
Language:Nextflow 131
nf-core / rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
nf-core nextflow workflow rna-seq rna pipeline fusion-genes fusion gene-fusion
Language:Nextflow 130
nf-core / fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
workflow nextflow nf-core pipeline fastq sra ena geo download synapse ddbj
Language:Nextflow 125
nf-core / eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
nextflow ancientdna adna pipeline pathogen-genomics population-genetics nf-core workflow metagenomics bioinformatics genome ancient-dna-analysis
Language:Nextflow 123
nf-core / viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
viral metagenomics amplicon assembly variant-calling illumina pipeline workflow nextflow nf-core covid-19 covid19 virus sars-cov-2 nanopore ont artic long-read-sequencing oxford-nanopore
Language:Nextflow 109
nf-core / taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
metagenomics profiling taxonomic-profiling shotgun nf-core nextflow workflow pipeline classification microbiome taxonomic-classification long-reads nanopore bioinformatics illumina pathogen
Language:Nextflow 93
nf-core / test-datasets
Test data to be used for automated testing with the nf-core pipelines
nextflow pipelines test-data testing test-datasets nf-core workflow
87
nf-core / configs
Config files used to define parameters specific to compute environments at different Institutions
nf-core nextflow configuration bioinformatics workflows pipelines
Language:Nextflow 77
nf-core / hic
Analysis of Chromosome Conformation Capture data (Hi-C)
nf-core nextflow hi-c chromosome-conformation-capture workflow pipeline
Language:Nextflow 75
nf-core / raredisease
Call and score variants from WGS/WES of rare disease patients.
nf-core nextflow workflow pipeline wgs wes variant-calling snv structural-variants variant-annotation diagnostics rare-disease
Language:Nextflow 72
nf-core / smrnaseq
A small-RNA sequencing analysis pipeline
nextflow nf-core pipeline small-rna smrna-seq workflow
Language:Nextflow 68
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 nextflow workflow pipeline cutandrun-seq cutandrun cutandtag-seq cutandtag
Language:Nextflow 65
nf-core / website
Code and files for the main nf-core website.
nf-core nextflow website
Language:Astro 62
nf-core / funcscan
(Meta-)genome screening for functional and natural product gene sequences
nextflow workflow pipeline assembly contigs function screening metagenomics natural-products antimicrobial-resistance-genes antimicrobial-peptides biosynthetic-gene-clusters bioinformatics amp antibiotic-resistance arg bgc secondary-metabolites amr nf-core
Language:Nextflow 56
nf-core / hlatyping
Precision HLA typing from next-generation sequencing data
hla hla-typing immunology dna rna optitype personalized-medicine nf-core nextflow workflow pipeline
Language:Nextflow 52
nf-core / bacass
Simple bacterial assembly and annotation pipeline
nf-core workflow nextflow pipeline genome-assembly bacterial-genomes assembly hybrid-assembly nanopore nanopore-sequencing denovo denovo-assembly
Language:Nextflow 51
nf-core / pangenome
Renders a collection of sequences into a pangenome graph.
nf-core nextflow workflow pipeline pangenome
Language:Nextflow 51
nf-core / bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
nf-core nextflow workflow pipeline bacteria bacterial bacterial-genome-analysis phylogeny mapping genomics tree
Language:Nextflow 48
nf-core / differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
nextflow nf-core pipeline workflow atac-seq chip-seq deseq2 differential-abundance differential-expression gsea limma microarray rna-seq shiny
Language:Nextflow 46
nf-core / airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
b-cell immcantation immunorepertoire repseq nf-core nextflow workflow pipeline airr
Language:Nextflow 43
nf-core / proteinfold
Protein 3D structure prediction pipeline
workflow protein-structure protein-sequences protein-folding protein-fold-prediction alphafold2 pipeline nextflow nf-core
Language:Nextflow 41
nf-core / circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
circrna circrna-prediction circrna-pipeline circular-rna rna-seq nf-core nextflow pipeline workflow bioinformatics ngs genomics mirna mirna-targets
Language:Nextflow 40
nf-core / deepvariant
Please consider using/contributing to https://github.com/nf-core/sarek
nf-core nextflow workflow pipeline deep-variant dna variant-calling google
Language:Nextflow 40
nf-core / spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
nf-core nextflow workflow pipeline 10x-genomics 10xgenomics bioinformatics image-processing microscopy rna-seq single-cell spatial spatial-transcriptomics st transcriptomics visium
Language:Nextflow 39
Midnighter / nextflow-gotchas
A collection of unexpected challenges and learnings with nextflow and nf-core.
nextflow nf-core nextflow-pipeline nextflow-process nextflow-workflow gotcha
Language:Shell 34
nf-core / rnasplice
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
nextflow nf-core pipeline workflow alternative-splicing rna rna-seq splicing
Language:Nextflow 34