Workflows

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131 Workflows visible to you, out of a total of 131
Assembly-Hifi-only-VGP3/main

Contiging Solo w/HiC:

Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.

Inputs

  1. Hifi long reads [fastq]
  2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
  3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
  4. K-mer database [meryldb]
  5. Genome profile summary generated by Genomescope [txt]
  6. Name of first assembly
  7. Name of second ...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Assembly-Hifi-Trio-phasing-VGP5/main

Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing

Inputs

  1. Hifi long reads [fastq]
  2. Concatenated Illumina reads : Paternal [fastq]
  3. Concatenated Illumina reads : Maternal [fastq]
  4. K-mer database [meryldb]
  5. Paternal hapmer database [meryldb]
  6. Maternal hapmer database [meryldb]
  7. Genome profile summary generated by Genomescope [txt]
  8. Genome model parameters generated by Genomescope [tabular]

...

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Assembly-decontamination-VGP9/main
No description specified

Type: Galaxy

Creator: Nadolina Brajuka

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

nanopore-pre-processing/main

Microbiome - QC and Contamination Filtering

Type: Galaxy

Creators: Bérénice Batut, Engy Nasr, Paul Zierep

Submitter: WorkflowHub Bot

DOI: 10.48546/workflowhub.workflow.1061.1

pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main

Pathogens of all samples report generation and visualization

Type: Galaxy

Creators: Engy Nasr, Bérénice Batut, Paul Zierep

Submitter: WorkflowHub Bot

DOI: 10.48546/workflowhub.workflow.1060.1

taxonomy-profiling-and-visualization-with-krona/main

Microbiome - Taxonomy Profiling

Type: Galaxy

Creators: Engy Nasr, Bérénice Batut, Paul Zierep

Submitter: WorkflowHub Bot

DOI: 10.48546/workflowhub.workflow.1059.1

Plot-Nx-Size/main

Generate Nx and Size plot for multiple assemblies

Inputs

Collection of fasta files. The name of each item in the collection will be used as label for the Nx and Size plots.

Outputs

  1. Nx plot
  2. Size plot

Type: Galaxy

Creators: Delphine Lariviere, VGP

Submitter: WorkflowHub Bot

nf-core/demo

An nf-core demo pipeline

Type: Nextflow

Creator: Christopher Hakkaart

Submitter: WorkflowHub Bot

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