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Nextflow Pipelines

Nextflow pipelines hosted in Git repositories. Each published release records the Git revision it runs and the launch configuration it ships with.

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9 pipeline(s) matching "ngs".

Pipeline Keywords Description
nf-core/circrna
0.0.0-23fdf1d
 circrna circrna-pipeline circrna-prediction circular-rna +5 circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
nf-core/crisprseq
2.3.0
 crispr crispr-analysis crispr-cas ngs A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
nf-core/denovohybrid
0.0.0-9299621
 assembly denovo denovo-assembly genome-assembly +4 UNDER CONSTRUCTION: Hybrid genome assembly pipeline using a combination of long and short sequencing reads
nf-core/fetchngs
1.13.0
 ddbj download ena fastq +3 Pipeline to fetch metadata and raw FastQ files from public databases
nf-core/hgtseq
1.1.0
 bwa-mem bwa-mem2 fastqc genomics-visualization +9 A pipeline to investigate horizontal gene transfer from NGS data
nf-core/oncoanalyser
3.0.0
 cancer clinical ctdna dna +9 A comprehensive cancer DNA/RNA analysis and reporting pipeline
nf-core/sammyseq
0.0.0-023aff4
 3d-genome chromatin dna epigenetics +6 Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
nf-core/vipr
0.0.0-6eef3b3
 genome-assembly metagenomics variant-calling viral +5 Assembly and intrahost / low-frequency variant calling for viral samples
nf-core/viralmetagenome
1.2.0
 epidemiology fastq ngs viral-metagenomics +2 A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Nextflow Registry v0.28.0_c73a300 - 12 Oct 2026 09:32:30 (UTC)