Workflows

What is a Workflow?
1196 Workflows visible to you, out of a total of 1279
MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data

Assembly and quantification metatranscriptome using metagenome data.

Version: see VERSION

Introduction

MetaGT is a bioinformatics analysis pipeline used for improving and quantification metatranscriptome assembly using metagenome data. The pipeline supports Illumina sequencing data and complete metagenome and metatranscriptome assemblies. The pipeline involves the alignment of metatranscriprome assembly to the metagenome assembly with further extracting CDSs, which are covered by ...

Type: Nextflow

Creators: Andrey Prjibelski, Varsha Kale, Anton Korobeynikov

Submitter: Varsha Kale

LongRead Quality Control and Filtering
Work-in-progress

Workflow for LongRead Quality Control and Filtering

  • NanoPlot (read quality control) before and after filtering
  • Filtlong (read trimming)
  • Kraken2 taxonomic read classification before and after filtering
  • Minimap2 read filtering based on given references

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

All tool CWL files and other workflows can be found here: https://gitlab.com/m-unlock/cwl/workflows

**How to setup and use an UNLOCK ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Germán Royval

Submitter: Bart Nijsse

Workflow for Illumina Quality Control and Filtering
Stable

Workflow for Illumina Quality Control and Filtering

Multiple paired datasets will be merged into single paired dataset.

Summary:

  • FastQC on raw data files
  • fastp for read quality trimming
  • BBduk for phiX and (optional) rRNA filtering
  • Kraken2 for taxonomic classification of reads (optional)
  • BBmap for (contamination) filtering using given references (optional)
  • FastQC on filtered (merged) data

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Changlin Ke

Submitter: Bart Nijsse

RASflow: RNA-Seq Analysis Snakemake Workflow
Stable

RASflow: RNA-Seq Analysis Snakemake Workflow

RASflow is a modular, flexible and user-friendly RNA-Seq analysis workflow.

RASflow can be applied to both model and non-model organisms. It supports mapping RNA-Seq raw reads to both genome and transcriptome (can be downloaded from public database or can be homemade by users) and it can do both transcript- and gene-level Differential Expression Analysis (DEA) when transcriptome is used as mapping reference. It requires little programming skill for ...

Type: Snakemake

Creator: Xiaokang Zhang

Submitter: Xiaokang Zhang

MGnify raw reads taxonomic profiling pipeline
Stable

The containerised pipeline for profiling shotgun metagenomic data is derived from the MGnify pipeline raw-reads analyses, a well-established resource used for analyzing microbiome data. Key components:

  • Quality control and decontamination
  • rRNA and ncRNA detection using Rfam database
  • Taxonomic classification of SSU and LSU regions
  • Abundance analysis with mOTUs

Type: Nextflow

Creators: Ekaterina Sakharova, Martin Beracochea

Submitter: Ekaterina Sakharova

GRAVI: Gene Regulatory Analysis using Variable Inputs
Work-in-progress

GRAVI: Gene Regulatory Analysis using Variable Inputs

This is a snakemake workflow for:

  1. Performing sample QC
  2. Calling ChIP peaks
  3. Performing Differential Binding Analysis
  4. Comparing results across ChIP targets

The minimum required input is one ChIP target with two conditions.

Full documentation can be found here

Snakemake Implementation

The basic workflow is written snakemake, requiring at least v7.7, and can be called using the following ...

Type: Snakemake

Creator: Stevie Pederson

Submitter: Stevie Pederson

DOI: 10.48546/workflowhub.workflow.443.1

SNP-Calling Workflow
Work-in-progress

SNP-Calling

GATK Variant calling pipeline for genomic data using Nextflow

nextflow

Quickstart

Install Nextflow using the following command:

curl -s https://get.nextflow.io | bash

Index reference genome:

$ bwa index /path/to/reference/genome.fa

$ samtools faidx /path/to/reference/genome.fa

$ gatk CreateSequenceDictionary -R /path/to/genome.fa -O genome.dict

Launch the pipeline execution with ...

Type: Nextflow

Creators: None

Submitter: Jeffrey Detras

IGVreport-nf
Work-in-progress

IGVreport-nf

Description

Quickly generate [IGV .html ...

Type: Nextflow

Creators: Georgina Samaha, Tracy Chew

Submitter: Georgina Samaha

Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation
Work-in-progress

ROIforMSI

Source codes for manuscript "Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation"

"ExampleWorkflow.ipynb" is a methods document to demonstrate the workflow of our multimodal fusion-based spatial segmentation.

"Utilities.py" contains all the tools to implement our method.

"gui.py" and "registration_gui.py" are files to implement linear and nonlinear registration.

(Licence: GPL-3)

Type: Python

Creators: Ang Guo, Qian Luo

Submitter: Ang Guo

DOI: 10.48546/workflowhub.workflow.437.1

Trio Analysis
Stable

To discover causal mutations of inherited diseases it’s common practice to do a trio analysis. In a trio analysis DNA is sequenced of both the patient and parents. Using this method, it’s possible to identify multiple inheritance patterns. Some examples of these patterns are autosomal recessive, autosomal dominant, and de-novo variants, which are represented in the figure below. To elaborate, the most left tree shows an autosomal dominant inhertitance pattern where the offspring inherits a faulty ...

Type: Galaxy

Creator: Jasper Ouwerkerk

Submitter: Helena Rasche

DOI: 10.48546/workflowhub.workflow.363.2

Powered by
 (v.1.17.0-main)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2025 The University of Manchester and HITS gGmbH