Workflows

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738 Workflows visible to you, out of a total of 793
ERGA-BGE Genome Report ASM analyses (one-asm HiFi + HiC)
Stable

Assembly Evaluation for ERGA-BGE Reports

One Assmebly, HiFi WGS reads + HiC reads

The workflow requires the following:

  • Species Taxonomy ID number
  • NCBI Genome assembly accession code
  • BUSCO Lineage
  • WGS accurate reads accession code
  • NCBI HiC reads accession code

The workflow will get the data and process it to generate genome profiling (genomescope, smudgeplot -optional-), assembly stats (gfastats), merqury stats (QV, completeness), BUSCO, snailplot, contamination blobplot, and HiC ...

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.1104.1

ERGA-BGE Genome Report ASM analyses (one-asm WGS Illumina PE + HiC)
Stable

Assembly Evaluation for ERGA-BGE Reports

One Assmebly, Illumina WGS reads + HiC reads

The workflow requires the following:

  • Species Taxonomy ID number
  • NCBI Genome assembly accession code
  • BUSCO Lineage
  • WGS accurate reads accession code
  • NCBI HiC reads accession code

The workflow will get the data and process it to generate genome profiling (genomescope, smudgeplot -optional-), assembly stats (gfastats), merqury stats (QV, completeness), BUSCO, snailplot, contamination blobplot, and ...

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.1103.2

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

Assembly-Hifi-only-VGP3/main

Contiging Solo:

Generate assembly based on PacBio Hifi Reads.

Inputs

  1. Hifi long reads [fastq]
  2. K-mer database [meryldb]
  3. Genome profile summary generated by Genomescope [txt]
  4. Homozygous Read Coverage. Optional, use if you think the estimation from Genomescope is inacurate.
  5. Genomescope Model Parameters generated by Genomescope [tabular]
  6. Database for busco lineage (recommended: latest)
  7. Busco lineage (recommended: vertebrata)
  8. Name of first assembly
  9. 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

RiboSnake: 16S rRNA analysis workflow with QIIME2 and Snakemake

RiboSnake: 16S rRNA analysis workflow with QIIME2 and Snakemake

Snakemake Build Status

Qiime2 workflow for 16S analysis created with snakemake.

Authors

  • Ann-Kathrin Dörr (@AKBrueggemann)

Usage

If you use this workflow in a paper, don't forget to give credits to the authors ...

Type: Snakemake

Creator: Ann-Kathrin Dörr

Submitter: Ann-Kathrin Dörr

DOI: 10.48546/workflowhub.workflow.1102.1

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

Random Forest Classifier executed in 3 nodes, 1 master and 2 workers, with a generated dataset, using 1 Million rows x 100 features

Name: Random Forest Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum4 This is an example of Random Forest algorithm from dislib. To show the usage, the code generates a synthetical input matrix. The results are printed by screen. This application used dislib-0.9.0

Type: COMPSs

Creator: Fernando Vázquez-Novoa

Submitter: Fernando Vázquez-Novoa

DOI: 10.48546/workflowhub.workflow.748.1

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