Workflows

What is a Workflow?

736 Workflows visible to you, out of a total of 791

Obitools eDNA metabarcoding

PNDB

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

Created: 9th Nov 2023 at 12:41

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

QCIF Bioinformatics

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

Created: 9th Nov 2023 at 05:26

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

QCIF Bioinformatics

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

Created: 9th Nov 2023 at 05:24

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

QCIF Bioinformatics

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

Created: 9th Nov 2023 at 05:20

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

QCIF Bioinformatics

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

Created: 9th Nov 2023 at 05:16

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

QCIF Bioinformatics

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

Created: 9th Nov 2023 at 05:04, Last updated: 9th Nov 2023 at 05:13

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

QCIF Bioinformatics

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

Created: 9th Nov 2023 at 05:11

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

Workflows and Distributed Computing

Stable

Name: Word Count Contact Person: support-compss@bsc.es 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

Created: 2nd Nov 2023 at 11:09, Last updated: 8th Nov 2023 at 15:46

Assembly-Hifi-HiC-phasing-VGP4/main

Intergalactic Workflow Commission (IWC)

Tests Not available

Contiging Solo w/HiC:

Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.

Inputs

Hifi long reads [fastq]
HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
K-mer database [meryldb]
Genome profile summary generated by Genomescope [txt]
Name of first assembly
Name of second assembly ...

Type: Galaxy

Creators: Delphine Lariviere, Galaxy, VGP

Submitter: WorkflowHub Bot

Created: 4th Nov 2023 at 03:01