Available Pipelines

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

2 nf-core/mhcquant

mass-spectrometry peptides

Identify and quantify peptides from mass spectrometry raw data

Version 1.0.0   Published 2 weeks ago

7 nf-core/deepvariant

deep-variant dna google variant-calling

Google's DeepVariant variant caller as a Nextflow pipeline

Version 1.0   Published 3 weeks ago

9 nf-core/eager

adna ancientdna pathogen-genomics population-genetics

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

Version 2.0.2   Published 1 month ago

60 nf-core/rnaseq

rna rna-seq

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

Version 1.1   Published 2 months ago

nf-core/hlatyping

dna hla hla-typing immunology optitype personalized-medicine rna

Precision HLA typing from next-generation sequencing data

Version 1.1.1   Published 4 months ago

17 nf-core/methylseq

bisulfite-sequencing dna-methylation methyl-seq

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

Version 1.1   Published 4 months ago

15 nf-core/ampliseq

16s amplicon-sequencing docker singularity

16S rRNA amplicon sequencing analysis workflow using QIIME2

No releases yet

nf-core/smrnaseq

small-rna smrna-seq

Analysis pipeline for small-RNA sequencing data.

No releases yet

2 nf-core/rnafusion

fusion fusion-genes gene-fusion rna rna-seq

RNA-seq analysis pipeline for detection gene-fusions

No releases yet

1 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/nascent

Nascent Transcription Processing Pipeline

No releases yet

7 nf-core/lncpipe

differential-expression lncrna rna-seq-analysis transcriptome

UNDER DEVELOPMENT--- A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets

No releases yet

6 nf-core/mag

annotation assembly binning bioinformatics metagenomics

UNDER CONSTRUCTION: Assembly, binning and annotation of metagenomes.

No releases yet

4 nf-core/atacseq

atac-seq chromatin-accessibiity

UNDER CONSTRUCTION: ATAC-seq peak-calling and differential analysis pipeline.

No releases yet

7 nf-core/exoseq

exome exome-sequencing genomics variant-calling

Exome Sequencing analysis pipeline (Work in progress)

No releases yet

nf-core/epitopeprediction

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

No releases yet

nf-core/ddamsproteomics

Quant proteomics as practiced at Lehtiƶ lab for NF-core

No releases yet

16 nf-core/chipseq

atac-seq chip chip-seq chromatin-immunoprecipitation peak-calling

Chromatin immunoprecipitation (ChIP-seq) analysis using BWA and MACS2 with QC steps.

No releases yet

nf-core/bcellmagic

B/T cell repertoire analysis pipeline with immcantation framework. WIP, currently requires a bunch of changes first.

No releases yet

4 nf-core/vipr

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

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

No releases yet

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