Available Pipelines
Can you think of another pipeline that would fit in well? Let us know!
135 nf-core/rnaseq
RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control
Version 1.4.2 Published 2 days ago
9 nf-core/sarek
cancer germline somatic variant-calling
An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing
Version 2.5 Published 2 weeks ago
8 nf-core/mhcquant
Identify and quantify peptides from mass spectrometry raw data
Version 1.3 Published 3 months ago
32 nf-core/ampliseq
16S rRNA amplicon sequencing analysis workflow using QIIME2
Version 1.1.0 Published 3 months 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 4 months ago
24 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 4 months ago
36 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 4 months ago
35 nf-core/rnafusion
fusion fusion-genes gene-fusion rna rna-seq
RNA-seq analysis pipeline for detection gene-fusions
Version 1.0.2 Published 5 months ago
11 nf-core/hic
chromosome-conformation-capture hi-c
Analysis of Chromosome Conformation Capture data (Hi-C)
Version 1.0.0 Published 5 months ago
8 nf-core/bacass
bacterial-genomes genome-assembly
Simple bacterial assembly and annotation pipeline.
Version 1.0.0 Published 5 months ago
2 nf-core/coproid
adna ancient-dna coprolite microbiome
Coprolite host Identification pipeline
Version 1.0 Published 6 months ago
3 nf-core/bcellmagic
B cell repertoire analysis pipeline with immcantation framework.
Version 1.0.0 Published 6 months ago
3 nf-core/nascent
gro-seq nascent pro-seq rna transcription
Nascent Transcription Processing Pipeline
Version 1.0 Published 6 months ago
22 nf-core/atacseq
atac-seq chromatin-accessibiity
ATAC-seq peak-calling, QC and differential analysis pipeline.
Version 1.0.0 Published 6 months ago
32 nf-core/methylseq
bisulfite-sequencing dna-methylation methyl-seq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Version 1.3 Published 9 months ago
23 nf-core/deepvariant
deep-variant dna google variant-calling
Google's DeepVariant variant caller as a Nextflow pipeline
Version 1.0 Published 11 months ago
1 nf-core/bactmap
WIP: A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
No releases yet
2 nf-core/proteomicslfq
label-free-quantification proteomics
UNDER CONSTRUCTION - Proteomics label-free quantification (LFQ) analysis pipeline
No releases yet
4 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
1 nf-core/nanodemux
alignment demultiplexing nanopore qc
UNDER CONSTRUCTION: Nanopore demultiplexing, QC and alignment pipeline.
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
15 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
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
14 nf-core/mag
annotation assembly binning metagenomics
Assembly and binning of metagenomes
No releases yet
7 nf-core/clinvap
annotation clinical variant-annotation
WIP: A Nextflow pipeline to perform clinical variant annotation and reporting.
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
2 nf-core/guideseq
UNDER CONSTRUCTION - CRISPR-Cas off-target identification using GUIDE-Seq
No releases yet
11 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
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
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
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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