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 7 days ago

37 nf-core/atacseq

atac-seq chromatin-accessibiity

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

Version 1.2.0   Published 7 days ago

18 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 2 weeks ago

52 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 2 weeks ago

5 nf-core/imcyto

cytometry image-analysis image-processing image-segmentation

Image Mass Cytometry analysis pipeline

Version 1.0.0   Published 1 month 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 2 months ago

45 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

15 nf-core/hic

chromosome-conformation-capture hi-c

Analysis of Chromosome Conformation Capture data (Hi-C)

Version 1.1.0   Published 9 months ago

201 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