What is a Workflow?
394 Workflows visible to you, out of a total of 425

This repository contains the python code to reproduce the experiments in Dłotko, Gurnari "Euler Characteristic Curves and Profiles: a stable shape invariant for big data problems"

Type: Python

Creator: Davide Gurnari

Submitter: Davide Gurnari

DOI: 10.48546/workflowhub.workflow.576.1

RepeatMasking Workflow

This workflow uses RepeatModeler and RepeatMasker for genome analysis.

  • RepeatModeler is a software package for identifying and modeling de novo families of transposable elements (TEs). At the heart of RepeatModeler are three de novo repeat search programs (RECON, RepeatScout and LtrHarvest/Ltr_retriever) which use complementary computational methods to identify repeat element boundaries and family relationships from sequence data.

  • RepeatMasker is a program that analyzes ...

Type: Galaxy

Creator: Romane Libouban

Submitter: WorkflowHub Bot

This workflow represents the Default ML Pipeline for AutoML feature from MLme. Machine Learning Made Easy (MLme) is a novel tool that simplifies machine learning (ML) for researchers. By integrating four essential functionalities, namely data exploration, AutoML, CustomML, and visualization, MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. MLme serves as a valuable resource that empowers researchers of all technical levels to leverage ...

Type: Workflow Description Language

Creator: Akshay Akshay

Submitter: Akshay Akshay

DOI: 10.48546/workflowhub.workflow.571.1

ERGA Protein-coding gene annotation workflow.

Adapted from the work of Sagane Joye:


The following programs are required to run the workflow and the listed version were tested. It should be noted that older versions of snakemake are not compatible with newer versions of singularity as is noted here:

conda v 23.7.3 ...

Type: Snakemake

Creator: Sagane Joye-Dind

Submitter: Tom Brown

DOI: 10.48546/workflowhub.workflow.569.1

Racon polish with long reads, x4

Type: Galaxy

Creator: Anna Syme

Submitter: WorkflowHub Bot

Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession.

Type: Galaxy

Creators: Marius van den Beek, IWC

Submitter: WorkflowHub Bot

This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using both subsets combined. Only peaks called using a combination of both subsets which have summits intersecting the intersection of both replicates will be kept.

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

This workflow takes as input a collection of paired fastqs. Remove adapters with cutadapt, map pairs with bowtie2. Keep MAPQ30 and concordant pairs. MACS2 for paired bam.

Type: Galaxy

Creators: Lucille Delisle, Lucille Delisle

Submitter: WorkflowHub Bot

This workflow takes as input a collection of fastqs (single reads). Remove adapters with cutadapt, map with bowtie2. Keep MAPQ30. MACS2 for bam with fixed extension or model.

Type: Galaxy

Creators: Lucille Delisle, Lucille Delisle

Submitter: WorkflowHub Bot


HiFi de novo genome assembly workflow

HiFi-assembly-workflow is a bioinformatics pipeline that can be used to analyse Pacbio CCS reads for de novo genome assembly using PacBio Circular Consensus Sequencing (CCS) reads. This workflow is implemented in Nextflow and has 3 major sections.

Please refer to the following documentation for detailed description of each workflow section:

  • [Adapter filtration and pre-assembly quality control ...

Type: Nextflow

Creators: Naga Kasinadhuni, Ziad Al Bkhetan, Martha Zakrzewski, Kenneth Chan, Uwe Winter, Johan Gustafsson

Submitter: Johan Gustafsson

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