Workflows

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745 Workflows visible to you, out of a total of 794
DLA-Collections-test
Work-in-progress

An example workflow for the Specimen Data Refinery tool, allowing an individual tool to be used

Type: Galaxy

Creators: Laurence Livermore, Oliver Woolland

Submitter: Oliver Woolland

DOI: 10.48546/workflowhub.workflow.374.1

De novo digitisation
Work-in-progress

An example workflow to allow users to run the Specimen Data Refinery tools on data provided in an input CSV file.

Type: Galaxy

Creators: Paul Brack, Oliver Woolland, Laurence Livermore

Submitter: Oliver Woolland

DOI: 10.48546/workflowhub.workflow.373.1

CNV_pipeline
Stable

StructuralVariants Workflow

Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, Daniel López-López

Submitter: Laura Rodriguez-Navas

VGP-meryldb-creation/main

VGP Workflow #1

This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.

Inputs

  • Collection of Hifi long reads in FASTQ format

Outputs

  • Meryl Database of kmer counts
  • GenomeScope
  • Linear plot

...

Type: Galaxy

Creators: None

Submitter: WorkflowHub Bot

VGP-meryldb-creation-trio/main

VGP Workflow #1

This workflow collects the metrics on the properties of the genome under consideration by analyzing the k-mer frequencies. It provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality. It uses reads from two parental genomes to partition long reads from the offspring into haplotype-specific k-mer databases.

Inputs

  • Collection of Hifi long reads in FASTQ format
  • Paternal short-read ...

Type: Galaxy

Creators: None

Submitter: WorkflowHub Bot

Workflow for running the Community Earth System Model in fully coupled mode
Stable

This workflow demonstrates the usage of the Community Earth System Model on Galaxy Europe.

A fully coupled B1850 compset with resolution f19_g17 is run for 1 month.

Type: Galaxy

Creators: None

Submitter: Anne Fouilloux

MGnify - raw-reads analysis pipeline
Stable

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...

Type: Common Workflow Language

Creators: Ekaterina Sakharova, Varsha Kale, Martin Beracochea, Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn

Submitter: Martin Beracochea

DOI: 10.48546/workflowhub.workflow.362.1

MGnify - amplicon analysis pipeline
Stable

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...

Type: Common Workflow Language

Creator: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn

Submitter: Martin Beracochea

MGnify - assembly analysis pipeline
Stable

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...

Type: Common Workflow Language

Creator: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn

Submitter: Martin Beracochea

HiFi de novo genome assembly workflow

HiFi de novo genome assembly workflow

HiFi-assembly-workflow is a bioinformatics pipeline that can be used to analyse Pacbio CCS reads for de novo genome assembly using PacBio Circular Consensus Sequencing (CCS) reads. This workflow is implemented in Nextflow and has 3 major sections.

Please refer to the following documentation for detailed description of each workflow section:

Type: Nextflow

Creators: None

Submitter: Naga Kasinadhuni

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