Workflows

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174 Workflows visible to you, out of a total of 174
nf-core/mag

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Type: Nextflow

Creators: No author provided, Hadrien Gourlé, Daniel Straub, Sabrina Krakau

Submitter: WorkflowHub Bot

nf-core/ampliseq

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Type: Nextflow

Creators: Daniel Straub, Alexander Peltzer

Submitter: WorkflowHub Bot

nf-core/variantbenchmarking

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Type: Nextflow

Creators: None

Submitter: WorkflowHub Bot

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

nf-core/genomeassembler

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Type: Nextflow

Creators: None

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

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

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

sars-cov-2-consensus-from-variation/COVID-19-CONSENSUS-CONSTRUCTION

Build a consensus sequence from FILTER PASS variants with intrasample allele-frequency above a configurable consensus threshold. Hard-mask regions with low coverage (but not consensus variants within them) and ambiguous sites.

Type: Galaxy

Creators: Wolfgang Maier, Wolfgang Maier

Submitter: WorkflowHub Bot

Assembly-Hifi-HiC-phasing-VGP4/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 assembly ...

Type: Galaxy

Creators: Delphine Lariviere, Galaxy, VGP

Submitter: WorkflowHub Bot

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