Workflows

What is a Workflow?
144 Workflows visible to you, out of a total of 144
nf-core/pairgenomealign

Pairwise alignment pipeline (genome to genome or reads to genome)

Type: Nextflow

Creators: charles-plessy , charles-plessy

Submitter: WorkflowHub Bot

Purge-duplicate-contigs-VGP6/main

Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Scaffolding-Bionano-VGP7/main

Scaffolding with Bionano

Scaffolding using Bionano optical map data

Inputs

  1. Bionano data [cmap]
  2. Estimated genome size [txt]
  3. Phased assembly generated by Hifiasm [gfa1]

Outputs

  1. Scaffolds
  2. Non-scaffolded contigs
  3. QC: Assembly statistics
  4. QC: Nx plot
  5. QC: Size plot

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Purge-duplicates-one-haplotype-VGP6b/main

Purge Duplicate Contigs

Purge contigs marked as duplicates by purge_dups in a single haplotype(could be haplotypic duplication or overlap duplication) This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)

Inputs

  1. Genomescope model parameters [txt] (Generated by the k-mer profiling workflow)
  2. Hifi long reads - trimmed [fastq] (Generated by Cutadapt in the contigging workflow)
  3. Assembly to purge (e.g. hap1) ...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

nf-core/denovotranscript

A pipeline for de novo transcriptome assembly of short reads from bulk RNA-seq

Type: Nextflow

Creator: Avani Bhojwani and Timothy Little

Submitter: WorkflowHub Bot

kmer-profiling-hifi-trio-VGP2/main

Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

kmer-profiling-hifi-VGP1/main

VGP Workflow #1

This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.

Inputs

  • A collection of Hifi long reads in FASTQ format
  • k-mer length
  • Ploidy

Outputs

  • Meryl Database of kmer counts

...

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis

This workflow

  • Reconstruct phylogeny (insert fragments in a reference)
  • Alpha rarefaction analysis
  • Taxonomic analysis

Type: Galaxy

Creators: Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ

Submitter: WorkflowHub Bot

allele-based-pathogen-identification/main

Microbiome - Variant calling and Consensus Building

Type: Galaxy

Creators: Engy Nasr, Bérénice Batut, Paul Zierep

Submitter: WorkflowHub Bot

DOI: 10.48546/workflowhub.workflow.1063.2

gene-based-pathogen-identification/main

Nanopore datasets analysis - Phylogenetic Identification - antibiotic resistance genes detection and contigs building

Type: Galaxy

Creators: Engy Nasr, Bérénice Batut, Paul Zierep

Submitter: WorkflowHub Bot

DOI: 10.48546/workflowhub.workflow.1062.1

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