Available Pipelines

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15 nf-core/hic

chromosome-conformation-capture hi-c

Analysis of Chromosome Conformation Capture data (Hi-C)

Version 1.2.1   Published 5 days ago

56 nf-core/chipseq

chip chip-seq chromatin-immunoprecipitation macs2 peak-calling

ChIP-seq peak-calling, QC and differential analysis pipeline.

Version 1.2.0   Published 2 weeks ago

38 nf-core/atacseq

atac-seq chromatin-accessibiity

ATAC-seq peak-calling, QC and differential analysis pipeline

Version 1.2.0   Published 2 weeks ago

20 nf-core/viralrecon

amplicon assembly covid-19 covid19 illumina metagenomics sars-cov-2 variant-calling viral virus

Assembly and intrahost/low-frequency variant calling for viral samples

Version 1.1.0   Published 3 weeks ago

53 nf-core/sarek

cancer germline somatic variant-calling

Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing

Version 2.6.1   Published 3 weeks ago

5 nf-core/imcyto

cytometry image-analysis image-processing image-segmentation

Image Mass Cytometry analysis pipeline

Version 1.0.0   Published 2 months ago

3 nf-core/slamseq

differential-expression quantseq slamseq transcriptomics

SLAMSeq processing and analysis pipeline

Version 1.0.0   Published 2 months ago

2 nf-core/coproid

adna ancient-dna coprolite microbiome

Coprolite host Identification pipeline

Version 1.1   Published 2 months ago

12 nf-core/mhcquant

mass-spectrometry mhc peptides

Identify and quantify MHC eluted peptides from mass spectrometry raw data

Version 1.5.1   Published 3 months ago

46 nf-core/methylseq

bisulfite-sequencing dna-methylation methyl-seq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

Version 1.5   Published 3 months ago

33 nf-core/eager

adna ancient-dna-analysis ancientdna genome metagenomics pathogen-genomics population-genetics

A fully reproducible and state of the art ancient DNA analysis pipeline

Version 2.1.0   Published 4 months ago

13 nf-core/nanoseq

alignment demultiplexing nanopore qc

Nanopore demultiplexing, QC and alignment pipeline

Version 1.0.0   Published 4 months ago

45 nf-core/rnafusion

fusion fusion-genes gene-fusion rna rna-seq

RNA-seq analysis pipeline for detection gene-fusions

Version 1.1.0   Published 5 months ago

10 nf-core/bcellmagic

b-cell immcantation immunorepertoire repseq

B cell repertoire sequencing analysis pipeline using the immcantation framework

Version 1.2.0   Published 6 months ago

18 nf-core/mag

annotation assembly binning metagenomics

Assembly and binning of metagenomes

Version 1.0.0   Published 7 months ago

40 nf-core/ampliseq

16s amplicon-sequencing metagenomics qiime rrna

16S rRNA amplicon sequencing analysis workflow using QIIME2

Version 1.1.2   Published 7 months ago

9 nf-core/bacass

bacterial-genomes genome-assembly

Simple bacterial assembly and annotation pipeline

Version 1.1.0   Published 7 months ago

3 nf-core/neutronstar

10x-genomics 10xgenomics denovo-assembly genome-assembly linked-reads supernova

De novo assembly pipeline for 10X linked-reads using Supernova

Version 1.0.0   Published 7 months ago

12 nf-core/scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

Version 1.0.0   Published 7 months ago

5 nf-core/epitopeprediction

epitope epitope-prediction mhc-binding-prediction

A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

Version 1.0.0   Published 7 months ago

204 nf-core/rnaseq

rna rna-seq

RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control

Version 1.4.2   Published 9 months ago

11 nf-core/smrnaseq

small-rna smrna-seq

A small-RNA sequencing analysis pipeline

Version 1.0.0   Published 10 months ago

11 nf-core/hlatyping

dna hla hla-typing immunology optitype personalized-medicine rna

Precision HLA typing from next-generation sequencing data

Version 1.1.5   Published 1 year ago

2 nf-core/nascent

gro-seq nascent pro-seq rna transcription

Nascent Transcription Processing Pipeline

Version 1.0   Published 1 year ago

28 nf-core/deepvariant

deep-variant dna google variant-calling

Google's DeepVariant variant caller as a Nextflow pipeline

Version 1.0   Published 2 years ago

11 nf-core/vipr

genome-assembly metagenomics variant-calling viral viral-genomics viral-metagenomics viral-ngs virus viruses

Assembly and intrahost / low-frequency variant calling for viral samples

No releases yet

3 nf-core/smartseq2

A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.

No releases yet

1 nf-core/bactmap

WIP: A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

No releases yet

2 nf-core/cageseq

cage cage-seq cageseq-data gene-expression rna

CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

No releases yet

7 nf-core/proteomicslfq

label-free-quantification proteomics

UNDER CONSTRUCTION - Proteomics label-free quantification (LFQ) analysis pipeline

No releases yet

nf-core/diaproteomics

data-independent-proteomics dia-proteomics proteomics

Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

No releases yet

8 nf-core/clinvap

annotation clinical variant-annotation

WIP: A Nextflow pipeline to perform clinical variant annotation and reporting

No releases yet

nf-core/crisprvar

[WIP] Evaluate outcomes from genome editing experiments

No releases yet

4 nf-core/ddamsproteomics

proteomics shotgun-ms

Quantitative shotgun MS proteomics

No releases yet

nf-core/metaboigniter

identification mass-spectrometry metabolomics quantification

UNDER CONSTRUCTION: MetaboIGNITER - Get your metabolomics analysis up and running

No releases yet

18 nf-core/lncpipe

differential-expression lncrna long-non-coding non-coding rna rna-seq-analysis transcriptome

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

No releases yet

4 nf-core/kmermaid

k-mer kmer kmer-counting kmer-frequency-count

k-mer similarity analysis pipeline

No releases yet

1 nf-core/demultiplex

10x bcl2fastq cellranger demultiplexing illumina

UNDER CONSTRUCTION: Demultiplexing pipeline for Illumina sequencing data

No releases yet

3 nf-core/artic

artic assembly covid-19 illumina nanopore

UNDER CONSTRUCTION: nf-core ARTIC field bioinformatics pipeline

No releases yet

1 nf-core/denovohybrid

assembly denovo denovo-assembly genome-assembly hybrid-assembly nanopore nanopore-sequencing ngs-pipeline

UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads

No releases yet

nf-core/gwas

A pipeline for Genome Wide Association Studies

No releases yet

10 nf-core/exoseq

exome exome-sequencing variant-calling

Please consider using/contributing to https://github.com/nf-core/sarek

No releases yet

3 nf-core/mnaseseq

mnase-seq nucleosome nucleosome-maps nucleosome-positioning

UNDER CONSTRUCTION: MNase-seq analysis pipeline using BWA and DANPOS2.

No releases yet

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