nf-core

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Pinned Repositories

ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Language:Nextflow225 163 394147
chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
Language:Nextflow227 158 208162
configs
Config files used to define parameters specific to compute environments at different Institutions
Language:Nextflow104 172 54333
mag
Assembly and binning of metagenomes
Language:Nextflow250 170 372142
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
Language:Nextflow385 207 2.5k932
proposals
Where new ideas for nf-core pipelines, special interest groups and more are proposed
8 11 503
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Language:Nextflow1.1k 170 748810
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Language:Nextflow501 146 837488
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
Language:Nextflow298 148 221204
tools
Python package with helper tools for the nf-core community.
Language:Python278 162 1.3k218

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
Language:Nextflow501 146 837488
nf-core/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
Language:Nextflow385 207 2.5k932
nf-core/tools
Python package with helper tools for the nf-core community.
Language:Python278 162 1.3k218
nf-core/mag
Assembly and binning of metagenomes
Language:Nextflow250 170 372142
nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Language:Nextflow225 163 394147
nf-core/atacseq
ATAC-seq peak-calling and QC analysis pipeline
Language:Nextflow213 160 176128
nf-core/eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Language:Nextflow186 173 46086
nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Language:Nextflow168 165 23859
nf-core/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
Language:Nextflow144 120 220139
nf-core/test-datasets
Test data to be used for automated testing with the nf-core pipelines
142 157 59445
nf-core/configs
Config files used to define parameters specific to compute environments at different Institutions
Language:Nextflow104 172 54333
nf-core/website
Code and files for the main nf-core website.
Language:MDX81 164 495253
nf-core/epitopeprediction
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
Language:Nextflow48 157 8629
nf-core/variantbenchmarking
Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
Language:Nextflow36 174 10419
nf-core/hgtseq
A pipeline to investigate horizontal gene transfer from NGS data
Language:Nextflow26 176 47
nf-core/phaseimpute
A bioinformatics pipeline to phase and impute genetic data
Language:Nextflow25 160 8121
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.
Language:Nextflow22 184 109
nf-core/genomeqc
Compare the quality of multiple genomes, along with their annotations.
Language:Nextflow18 16 7916
nf-core/createtaxdb
Parallelised and automated construction of metagenomic classifier databases of different tools
Language:Nextflow15 178 4910
nf-core/seqinspector
QC pipeline to inspect your sequences
Language:Nextflow14 172 3735
nf-core/molkart
A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
Language:Nextflow13 167 4812
nf-core/metapep
From metagenomes to epitopes and beyond
Language:Nextflow12 84 3310
nf-core/rnadnavar
Pipeline for RNA and DNA integrated analysis for somatic mutation detection
Language:Nextflow11 158 810
nf-core/meerpipe
nf-core/meerpipe is a astronomy pipeline that processes MeerKAT pulsar data to produce images and data products for pulsar timing analysis
Language:Nextflow10 196 26
nf-core/logos
Host nf-core logos and templates for making new logos
7 191 514
nf-core/lsmquant
A pipeline for processing and analysis of light-sheet microscopy images.
Language:Nextflow51
nf-core/sammyseq
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
Language:Nextflow5 171 3617
nf-core/ops
Different *Ops related scripts for the nf-core org.
Language:Python3 7 882
nf-core/panoramaseq
a pipeline to process sequencing based spatial transccriptomics data from in-situ arrays
Language:HTML
nf-core/rarevariantburden
Pipeline for performing consistent summary count based rare variant burden test, which is useful when we only have sequenced cases data. For example, we can compare the cases against public summary count data, such as gnomAD.
Language:Nextflow2