Workflows

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844 Workflows visible to you, out of a total of 923
Extended Source
Stable

Calculate extended gamma-ray source halo using crbeam simulation

Type: Galaxy

Creators: None

Submitter: Oleg Kalashev

Purge-duplicates-one-haplotype-VGP6b/main

Purge contigs marked as duplicates by purge_dups in a single haplotype (could be haplotypic duplication or overlap duplication). If you think the purged contigs might belong to the other haplotype, use the workflow VGP6 instead. 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

Assembly-Hifi-Trio-phasing-VGP5/main

Generate phased assembly based on PacBio HiFi reads and parental Illumina data for phasing. Part of the VGP workflow suite, it needs to be run after the Trio k-mer Profiling workflow VGP2. This workflow uses HiFiasm for contigging, and generates assembly statistics, BUSCO reports, Merqury plots, and the genome assembly contigs in fasta and GFA format.

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Assembly-Hifi-only-VGP3/main

Generate a genome assembly based on PacBio HiFi reads. Part of the VGP suite, it needs to be run after the VGP1 k-mer profiling workflow. The assembly contigs are built using HiFiasm, and the workflow generates assembly statistics, BUSCO reports, Merqury plots, and the contigs in fasta and GFA formats.

Type: Galaxy

Creator: Galaxy, VGP

Submitter: WorkflowHub Bot

Purge-duplicate-contigs-VGP6/main

Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). The contigs are purged from the first assembly (hap1, pri...), added to the second assembly (hp2, alt... ), then the 2nd assembly is purged as well. If you think only one of the assemblies needs purging, use the VGP6b workflow. 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

Assembly-decontamination-VGP9/main

Decontamination (foreign contaminants and mitochondrial sequences) of a genome assembly after the final scaffolding step. Uses Kraken2 to identify foreign contaminants and Blast to identify mitochondrial sequences. Part of the VGP Suite.

Type: Galaxy

Creator: Nadolina Brajuka

Submitter: WorkflowHub Bot

Scaffolding-HiC-VGP8/main

This workflow performs the scaffolding of a genome assembly using HiC data with YAHS. Can be used on any assembly with Hi-C data, and the assembly in the gfa format. You can generate a gfa from a fasta using the gfastat tool. Part of the VGP set of workflows, it is meant to be run after the contigging (workflows 3,4, or 5), optional purging step (Workflow 6 or 6b), and an optionnal scaffolding with Bionano data (Workflow 7). This workflow includes QC with Assembly statistics, Busco, and Hi-C maps. ...

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

Mitogenome-assembly-VGP0/main

Generate mitochondrial assembly based on PacBio HiFi reads. Part of the VGP suite, it can be run at any time independently of the other workflows. This workflow uses MitoHiFi and a mitochondrial reference to assemble the mitochondrial genome from PacBio reads. You do not need to provide the reference yourself, only the Latin name of a closely related species.

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

Consensus Virtual Drug Screening Workflow

This workflows contains a pipeline in Scipion that performs the following steps:

1.1) Import small molecules: introduces a set of small molecular structures in the pipeline as prospective ligands

1.2) Import atomic structure: introduces a protein atomic structure in the pipeline as receptor.

2.1) Ligand preparation: uses RDKit to prepare the small molecules optimizing their 3D structure.

2.2) Receptor preparation: uses bioPython to prepare the receptor structure, removing waters, adding hydrogens ...

Type: Scipion

Creators: None

Submitter: Daniel Del Hoyo

Basic Virtual Drug Screening Workflow
Work-in-progress

This workflow performs the most basic Virtual Drug Screening Pipeline to import a set of small molecules and dock them to an imported protein structure.

Type: Scipion

Creators: None

Submitter: Daniel Del Hoyo

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