All Published Workflows

18 workflows that have been reviewed and published

nanopype
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Snakemake pipelines for nanopore sequencing data archiving and processing
public

public

Detailed documentation and tutorials are available at readthedocs . Nanopype is a snakemake based pipeline providing conv...
Sample annotation Base-calling Alignment sniffles svim bedGraphToBigWig BEDTools Flye GUPPY Minimap2 nanopolish NGMLR Pandas Racon SAMtools Singularity Hub Snakemake wtdbg2 graphmap2 matplotlib numpy oschmod seaborn nanopore
Free
87
methplotlib
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Plotting tools for nanopore methylation data
public

public

This script generates a browser view on a window using data from i) nanopolish , either as methylation calls or methylati...
GTF Text data Methylation analysis Plot nanopolish Snakemake nanopore
Free
3
score-assemblies
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Score and compare multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
public

public

A snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina seque...
bacterial Genome assembly Genome report nucdiff prodigal Bakta BUSCO Diamond Minimap2 QUAST SAMtools seqkit Snakemake ggplot2 tidyverse Comparative genomics nanopore
Free
32
single-cell-nanopore
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Workflow for Nanopore Sequencing of 10x single cell libraries
public

public

ScNapBar (single-cell Nanopore barcode demultiplexer) is a workflow to assign barcodes to long-read single-cell sequencing...
Sample annotation Sequencing quality control Quality control report BEDTools Minimap2 Pandas SAMtools Snakemake caret e1071 stringdist numpy scipy nanopore
Free
31
ont-assembly-snake
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Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools
public

public

A snakemake-wrapper for easily creating de novo bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, a...
FASTQ-illumina bacterial Genome assembly Sequence assembly report rasusa BWA CANU Diamond Filtlong Flye Medaka Minimap2 pilon proovframe Racon Raven SAMtools Snakemake Unicycler nanopore
Free
24
cyrcular-calling
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A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circular DNA.
public

public

A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circu...
Sample annotation Sequencing quality control Report rust-bio-tools snakemake-wrapper-utils BCFtools Pandas SAMtools Snakemake Varlociraptor nanopore
Free
44
ont_pipelines
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Oxford Nanopore Variant Calling and Methylation Pipeline
public

public

This is a Snakemake pipeline designed to take Oxford Nanopore Technologies data from fastq's to variant calls. In additions t...
Variant calling sniffles svim tabix BCFtools Minimap2 SAMtools Snakemake cuteSV pysam nanopore
Free
16
np_read_clustering
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Nanopore Read Clustering and Polishing Workflow
public

public

This workflow attempts to find clusters of similar sequences in a set of nanopore reads. It is intended to be used for sample...
prodigal Biopython MCL Medaka Minimap2 Pandas Snakemake edl matplotlib numpy scipy nanopore
Free
9
ngs_bench
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FABLE: An Automated Snakemake Workflow for Oxford Nanopore Sequencing Data Analysis
public

public

**FABLE is an automated and reproducible snakemake workflow tailored to Oxford Nanopore Sequencing reads. After easy installa...
porechop bedGraphToBigWig BEDTools FastQC Minimap2 MultiQC NanoPlot Pandas SAMtools Snakemake matplotlib numpy Sequence analysis nanopore
Free
28
fable
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FABLE: Automated and reproducible snakemake workflow
public

public

FABLE is an automated and reproducible snakemake workflow tailored to Oxford Nanopore Sequencing reads. After easy installation
porechop bedGraphToBigWig BEDTools FastQC Minimap2 MultiQC NanoPlot Pandas SAMtools Snakemake matplotlib numpy nanopore
Free
28
svont-pipeline
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SVONT-Pipeline: Structural Variant Detection and Annotation from Oxford Nanopore Data using Snakemake
public

public

SVONT-pipeline is pipeline for structural variant detection and annotation using Oxford Nanopore data . Oxford Nanopore T...
nanostat sniffles AnnotSV Minimap2 NanoPlot nanopolish SAMtools Snakemake nanopore
Free
10
seenv
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SeeNV: A Structural Variant Visualization and Analysis Tool for Oxford Nanopore Data
public

public

SeeNV is still being developed. It can be download and used but is by no means exaustively tested. Find a bug? Create an is...
tabix BEDTools mosdepth Pandas RepeatMasker SAMtools Snakemake matplotlib numpy pysam utils nanopore
Free
36