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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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12 pipeline(s) matching "ont".

Pipeline Keywords Description
nf-core/ampliseq
3.0.0
 16s 18s amplicon-sequencing edna +12 Amplicon sequencing analysis workflow using DADA2 and QIIME2
nf-core/detaxizer
1.3.0
 de-identification decontamination edna fastq +10 A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
nf-core/evexplorer
0.0.0-c5677f2
 extracellular-vesicles ont nf-core/evexplorer is a pipeline for analyzing RNA data from extracellular vesicles, compatible with technologies such as nextflex, comboSeq, and ONT with further support forthcoming. evexplorer handles QC, expressed region detection, library size normalization and Differential RNA Expression (DRE)
nf-core/funcscan
4.0.0
 amp amr antibiotic-resistance antimicrobial-peptides +11 (Meta-)genome screening for functional and natural product gene sequences
nf-core/genomeqc
1.0.1
 genome-assembly-evaluation genomics phylogenetic-trees quality-control Compare the quality of multiple genomes, along with their annotations.
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/methylong
2.0.0
 dna-methylation fiber-seq long-read ont +1 Extract methylation calls from long reads (ONT/ PacBio)
nf-core/rarevariantburden
0.0.0-3ba9926
 burden-test cocorv public-data-as-controlset rarevariant Pipeline for performing consistent summary count based rare variant burden test, which is useful when we only have sequenced cases data. For example, we can compare the cases against public summary count data, such as gnomAD.
nf-core/scdownstream
0.0.0-3c2644c
 clustering dimensionality-reduction integration quality-control +2 A single cell transcriptomics pipeline for QC, integration and making the data presentable
nf-core/seqinspector
1.1.2
 genomics quality-control Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core facilities or research groups with larger sequencing throughput.
nf-core/tumourevo
1.0.0
 cancer-evolution cancer-genomics copy-number-variation mutational-signatures +4 Analysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)
nf-core/viralrecon
3.0.0
 amplicon artic assembly covid-19 +11 Assembly and intrahost/low-frequency variant calling for viral samples
Nextflow Registry v0.28.0_c73a300 - 12 Oct 2026 09:32:30 (UTC)