Available Pipelines

Can you think of another pipeline that would fit in well? Let us know!

5 nf-core/mhcquant

mass-spectrometry peptides

Identify and quantify peptides from mass spectrometry raw data

Version 1.3   Published 2 weeks ago

30 nf-core/ampliseq

16s amplicon-sequencing qiime

16S rRNA amplicon sequencing analysis workflow using QIIME2

Version 1.1.0   Published 1 month ago

8 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 2 months ago

20 nf-core/eager

adna ancientdna pathogen-genomics population-genetics

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

Version 2.0.7   Published 2 months ago

33 nf-core/chipseq

chip chip-seq chromatin-immunoprecipitation macs2 peak-calling

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

Version 1.0.0   Published 2 months ago

32 nf-core/rnafusion

fusion fusion-genes gene-fusion rna rna-seq

RNA-seq analysis pipeline for detection gene-fusions

Version 1.0.2   Published 3 months ago

8 nf-core/hic

chromosome-conformation-capture hi-c

Analysis of Chromosome Conformation Capture data (Hi-C)

Version 1.0.0   Published 3 months ago

8 nf-core/bacass

bacterial-genomes genome-assembly

Simple bacterial assembly and annotation pipeline.

Version 1.0.0   Published 3 months ago

2 nf-core/coproid

adna ancient-dna coprolite microbiome

Coprolite host Identification pipeline

Version 1.0   Published 4 months ago

3 nf-core/bcellmagic

b-cell immcantation immune

B cell repertoire analysis pipeline with immcantation framework.

Version 1.0.0   Published 4 months ago

3 nf-core/nascent

gro-seq nascent pro-seq rna transcription

Nascent Transcription Processing Pipeline

Version 1.0   Published 4 months ago

21 nf-core/atacseq

atac-seq chromatin-accessibiity

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

Version 1.0.0   Published 4 months ago

124 nf-core/rnaseq

rna rna-seq

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

Version 1.3   Published 5 months ago

29 nf-core/methylseq

bisulfite-sequencing dna-methylation methyl-seq

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

Version 1.3   Published 6 months ago

22 nf-core/deepvariant

deep-variant dna google variant-calling

Google's DeepVariant variant caller as a Nextflow pipeline

Version 1.0   Published 9 months ago

7 nf-core/clinvap

annotation clinical variant-annotation

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

No releases yet

5 nf-core/smrnaseq

small-rna smrna-seq

UNDER CONSTRUCTION: Analysis pipeline for small-RNA sequencing data.

No releases yet

4 nf-core/scrnaseq

WIP: A single-cell RNAseq pipeline for 10X genomics data

No releases yet

2 nf-core/sarek

cancer germline somatic variant-calling

WIP: An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing

No releases yet

2 nf-core/proteomicslfq

label-free-quantification proteomics

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

No releases yet

3 nf-core/neutronstar

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

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

No releases yet

nf-core/mnaseseq

mnase-seq nucleosome nucleosome-maps nucleosome-positioning

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

No releases yet

1 nf-core/bactmap

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

No releases yet

14 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

12 nf-core/mag

annotation assembly binning metagenomics

Assembly and binning of metagenomes

No releases yet

nf-core/kmermaid

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

k-mer similarity analysis pipeline.

No releases yet

nf-core/imcyto

cytometry image-analysis image-processing image-segmentation

UNDER CONSTRUCTION: Image Mass Cytometry analysis pipeline

No releases yet

1 nf-core/guideseq

crispr crispr-cas9 guide-seq

UNDER CONSTRUCTION - CRISPR-Cas off-target identification using GUIDE-Seq

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/epitopeprediction

epitope epitopes-prediction

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

No releases yet

1 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

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

4 nf-core/ddamsproteomics

proteomics shotgun-ms

Quant proteomics as practiced at Lehtiƶ lab for nf-core

No releases yet

nf-core/crisprvar

[WIP] Evaluate outcomes from genome editing experiments

No releases yet

7 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

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