Workflows

What is a Workflow?

180 Workflows visible to you, out of a total of 180

hi-c-contact-map-for-assembly-manual-curation/main

This workflow generates Hi-C contact maps for genome assemblies in the Pretext format. It is compatible with one or 2 haplotypes. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.

Type: Galaxy

Creators: Patrik Smeds, Delphine Lariviere

Submitter: WorkflowHub Bot

Created: 29th Mar 2025 at 03:01

Plot-Nx-Size/main

Intergalactic Workflow Commission (IWC)

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

Nx plot
Size plot

Type: Galaxy

Creators: Delphine Lariviere, VGP

Submitter: WorkflowHub Bot

Created: 24th Jun 2024 at 03:01, Last updated: 26th Mar 2025 at 10:06

allele-based-pathogen-identification/main

Intergalactic Workflow Commission (IWC)

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

Created: 26th Jun 2024 at 03:02, Last updated: 26th Mar 2025 at 10:06

Assembly-Hifi-HiC-phasing-VGP4/main

Intergalactic Workflow Commission (IWC)

Contiging Solo w/HiC:

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

Inputs

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

Type: Galaxy

Creators: Delphine Lariviere, Galaxy, VGP

Submitter: WorkflowHub Bot

Created: 4th Nov 2023 at 03:01, Last updated: 26th Mar 2025 at 10:06