Workflows

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831 Workflows visible to you, out of a total of 904
Obitools eDNA metabarcoding
Stable

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Metabarcoding/eDNA through Obitools" .

This workflow allows to analyze DNA metabarcoding / eDNA data produced on Illumina sequencers using the OBITools.

Type: Galaxy

Creators: Yvan Le Bras, Coline Royaux

Submitter: Yvan Le Bras

DOI: 10.48546/workflowhub.workflow.655.1

Workflow 7 : Beta Diversity [16S Microbial Analysis With Mothur]

The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.

Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...

Type: Galaxy

Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi

Submitter: Sarah Williams

Workflow 6: Alpha Diversity [16S Microbial Analysis With Mothur]

The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.

Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...

Type: Galaxy

Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi

Submitter: Sarah Williams

Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur]

The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.

Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...

Type: Galaxy

Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi

Submitter: Sarah Williams

Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]

The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.

Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...

Type: Galaxy

Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi

Submitter: Sarah Williams

Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur]

16S Microbial Analysis with mothur (short)

The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for piepline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.

Please also refer to the 16S tutorials available at Galaxy ...

Type: Galaxy

Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi

Submitter: Sarah Williams

Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur]

The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for piepline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.

Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...

Type: Galaxy

Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi

Submitter: Sarah Williams

PyCOMPSs Wordcount test, using files as task inputs, and dictionaries as task outputs (executed at Marenostrum IV supercomputer)
Stable

Name: Word Count Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs

Description

Wordcount is an application that counts the number of words for a given set of files.

To allow parallelism every file is treated separately and merged afterwards.

Execution instructions

Usage:

runcompss --lang=python src/wordcount.py datasetPath

where:

  • datasetPath: Absolute path of the file to parse (e.g. /home/compss/tutorial_apps/python/wordcount/data/) ...

Type: COMPSs

Creators: Javier Conejero, The Workflows and Distributed Computing Team (https://www.bsc.es/discover-bsc/organisation/scientific-structure/workflows-and-distributed-computing/)

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.635.1

Autosubmit mHM test domains
Work-in-progress

Autosubmit mHM test domains

Type: Autosubmit

Creator: Bruno P. Kinoshita

Submitter: Bruno P. Kinoshita

ERGA HiC Hap1Hap2 Scaffolding+QC YaHS v2309 (WF4)
Stable

The workflow takes trimmed HiC forward and reverse reads, and Hap1/Hap2 assemblies to produce Hap1 and Hap2 scaffolded assemblies using YaHS. It also runs all the QC analyses (gfastats, BUSCO, Merqury and Pretext).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.608.1

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