Available Pipelines

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

13 nf-core/chipseq

chip-seq chromatin-immunoprecipitation peak-calling

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

No releases yet

7 nf-core/eager

adna ancientdna best-practice pathogen-genomics population-genetics

WORK IN PROGRESS: Hopefully soon a fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.

No releases yet

6 nf-core/exoseq

exome exome-sequencing genomics variant-calling

Exome Sequencing analysis pipeline (Work in progress)

No releases yet

0 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 1 month ago

5 nf-core/mag

annotation assembly binning bioinformatics metagenomics

UNDER CONSTRUCTION: Assembly, binning and annotation of metagenomes.

No releases yet

15 nf-core/methylseq

bisulfite-sequencing dna-methylation methyl-seq

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

Version 1.1   Published 1 month ago

40 nf-core/rnaseq

rna rna-seq

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

Version 1.0   Published 1 month ago

0 nf-core/smrnaseq

small-rna smrna-seq

Analysis pipeline for small-RNA sequencing data.

No releases yet

3 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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