nf-core

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150 repositories

fastqrepair
Public
A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered
corruption fastq-format fastq data-cleaning data-recovery well-formed recovery-tool fastq-corrupted unpaired-reads reads-interleaving
Nextflow
•
MIT License
•2•1•5•1•Updated Jan 25, 2025Jan 25, 2025
funcscan
Public
(Meta-)genome screening for functional and natural product gene sequences
workflow bioinformatics pipeline nextflow amp assembly function metagenomics amr screening
Nextflow
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MIT License
•22•78•15•2•Updated Jan 25, 2025Jan 25, 2025
modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
modules nextflow pipelines workflows nf-core dsl2 nf-test
Nextflow
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MIT License
•743•290•460•177•Updated Jan 25, 2025Jan 25, 2025
website
Public
Code and files for the main nf-core website.
website nextflow nf-core
MDX
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MIT License
•208•69•90•34•Updated Jan 25, 2025Jan 25, 2025
mag
Public
Assembly and binning of metagenomes
workflow nanopore annotation nextflow metagenomics binning nanopore-sequencing nf-core long-read-sequencing bioinformatics
Nextflow
•
MIT License
•115•226•58•11•Updated Jan 25, 2025Jan 25, 2025
test-datasets
Public
Test data to be used for automated testing with the nf-core pipelines
testing workflow nextflow test-data nf-core pipelines test-datasets
MIT License
•364•112•31•16•Updated Jan 25, 2025Jan 25, 2025
dualrnaseq
Public
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
workflow rna-seq pipeline nextflow quantification nf-core host-pathogen dualrna-seq readmapping
Nextflow
•
MIT License
•33•20•15•8•Updated Jan 25, 2025Jan 25, 2025
setup-nextflow
Public
A GitHub action to install Nextflow
nextflow actions
TypeScript
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MIT License
•6•14•9•5•Updated Jan 25, 2025Jan 25, 2025
pacvar
Public
Longread PacBio sequencing processing for WGS and PureTarget
alignment long-read pacbio variant-calling wgs puretarget
Nextflow
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MIT License
•2•3•1•2•Updated Jan 24, 2025Jan 24, 2025
rnaseq
Public
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
workflow rna-seq pipeline nextflow rna nf-core
Nextflow
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MIT License
•719•965•64•13•Updated Jan 24, 2025Jan 24, 2025
spatialxe
Public
Nextflow
•
MIT License
•3•7•30•2•Updated Jan 24, 2025Jan 24, 2025
variantbenchmarking
Public
A nextflow variant benchmarking pipeline - premature
workflow benchmark pipeline nextflow draft variant-calling structural-variants nf-core
Nextflow
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MIT License
•9•14•19•2•Updated Jan 24, 2025Jan 24, 2025
configs
Public
Config files used to define parameters specific to compute environments at different Institutions
bioinformatics nextflow configuration pipelines workflows nf-core
Nextflow
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MIT License
•283•93•12•15•Updated Jan 24, 2025Jan 24, 2025
tools
Public
Python package with helper tools for the nf-core community.
bioinformatics linting linter nf-core python workflow pipeline nextflow
Python
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MIT License
•192•246•272•41•Updated Jan 24, 2025Jan 24, 2025
ops
Public
Python
•2•1•45•8•Updated Jan 24, 2025Jan 24, 2025
riboseq
Public
Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•8•12•15•1•Updated Jan 24, 2025Jan 24, 2025
eager
Public
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
workflow metagenomics population-genetics adna pathogen-genomics nf-core ancientdna bioinformatics pipeline genome
Nextflow
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MIT License
•82•155•38•7•Updated Jan 24, 2025Jan 24, 2025
metatdenovo
Public
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
workflow pipeline nextflow metagenomics viruses metatranscriptomics prokaryotes eukaryotes nf-core
Nextflow
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MIT License
•11•23•11•1•Updated Jan 24, 2025Jan 24, 2025
stableexpression
Public
Pipeline dedicated to finding the most stable genes among a single or multiple expression dataset(s). It is useful in particular for finding the most suitable qPCR reference genes for a specific species.
workflow nextflow expression nf-core qpcr-analysis
Nextflow
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MIT License
•1•2•0•0•Updated Jan 24, 2025Jan 24, 2025
pairgenomealign
Public
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
bioinformatics genomics nextflow comparative-genomics synteny last pairwise-alignment whole-genome-alignment nf-core dot-plot
Nextflow
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MIT License
•3•6•10•0•Updated Jan 24, 2025Jan 24, 2025
stats
Public
evidence
HTML
•0•0•14•9•Updated Jan 24, 2025Jan 24, 2025
pathogensurveillance
Public
Surveillance of pathogens using population genomics and sequencing
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•6•15•43•0•Updated Jan 23, 2025Jan 23, 2025
pixelator
Public
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
nextflow proteins pixelator single-cell nf-core single-cell-omics molecular-pixelation pixelgen-technologies workflow pipeline
Nextflow
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MIT License
•4•8•0•1•Updated Jan 23, 2025Jan 23, 2025
mhcquant
Public
Identify and quantify MHC eluted peptides from mass spectrometry raw data
workflow pipeline nextflow dda mhc mass-spectrometry openms peptides nf-core immunopeptidomics
Nextflow
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MIT License
•27•33•10•1•Updated Jan 23, 2025Jan 23, 2025
createtaxdb
Public
Parallelised and automated construction of metagenomic classifier databases of different tools
workflow database pipeline nextflow metagenomics profiling nf-core database-builder taxonomic-profiling metagenomic-profiling
Nextflow
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MIT License
•7•8•15•3•Updated Jan 23, 2025Jan 23, 2025
pangenome
Public
Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.
workflow pipeline nextflow pangenome nf-core
Nextflow
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MIT License
•18•80•12•3•Updated Jan 23, 2025Jan 23, 2025
taxprofiler
Public
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
workflow bioinformatics nanopore pipeline nextflow shotgun pathogen metagenomics classification profiling
Nextflow
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MIT License
•38•134•40•6•Updated Jan 23, 2025Jan 23, 2025
multiplesequencealign
Public
A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.
workflow pipeline nextflow nf-core
Nextflow
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MIT License
•12•25•6•1•Updated Jan 23, 2025Jan 23, 2025
nanostring
Public
An analysis pipeline for Nanostring nCounter expression data.
workflow pipeline nextflow nanostring nanostringnorm nf-core
Nextflow
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MIT License
•10•13•6•1•Updated Jan 23, 2025Jan 23, 2025
sarek
Public
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
bioinformatics annotation genomics nextflow cancer reproducible-research containers conda next-generation-sequencing variant-calling
Nextflow
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MIT License
•421•417•269•37•Updated Jan 23, 2025Jan 23, 2025