Independent Teams
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Web page: Not specified
Funding details: Related items
Teams: CO2MICS Lab
Organizations: Biomedical Research Foundation (BRFAA) of the Academy of Athens
https://orcid.org/0000-0002-1761-8881
Teams: UX trial team
Organizations: The University of Manchester
Medical bioinformatics group of the Medical Proteome Center at the Ruhr University Bochum
Space: Independent Teams
Public web page: https://www.ruhr-uni-bochum.de/mpc/forschung/medical_bioinformatics/index.html.en
Space: Independent Teams
Public web page: Not specified
Team for URGI members, for testing/exploring mainly.
Space: Independent Teams
Public web page: https://www6.versailles-grignon.inrae.fr/urgi/
Space: Independent Teams
Public web page: https://www.elixir-belgium.org/
Space: Independent Teams
Public web page: https://x-omics.nl/
Country: Not specified
City: Not specified
Web page: Not specified
Download all genome from https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide with filter host:viridiplantae and Refseq on.
Creator: johan Rollin
Submitter: johan Rollin
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Abstract (Expand)
Authors: Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Carole Goble
Date Published: 14th May 2021
Publication Type: Unpublished
Abstract
Authors: Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft
Date Published: 2021
Publication Type: Journal
Abstract
Authors: Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober
Date Published: 2020
Publication Type: Journal
External Link
Creator: panou@fleming.gr Panou
Submitter: panou@fleming.gr Panou
Creator: johan Rollin
Submitter: johan Rollin
Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning
- Workflow Nanopore Quality
- Kraken2 taxonomic classification of FASTQ reads
- Flye (de-novo assembly)
- Medaka (assembly polishing)
- metaQUAST (assembly quality reports)
When Illumina reads are provided:
- Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
- Assembly polishing with Pilon
- Workflow binnning https://workflowhub.eu/workflows/64?version=11
- Metabat2 ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Jasper Koehorst
Workflow (hybrid) metagenomic assembly and binning
- Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
- FastQC (control)
- fastp (quality trimming)
- kraken2 (taxonomy)
- bbmap contamination filter
- Kraken2 taxonomic classification of FASTQ reads
- SPAdes (Assembly)
- QUAST (Assembly quality report)
- BBmap (Read mapping to assembly)
- Workflow binnning https://workflowhub.eu/workflows/64?version=11
- Metabat2
- CheckM
- BUSCO
- GTDB-Tk
**All tool CWL files and other ...
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.
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:
Generic consensus building
This workflow generates consensus sequences using a list of variants generated by Variant Calling Workflow.
The workflow accepts a single input:
- A collection of VCF files
The workflow produces a single output:
- Consensus sequence for each input VCF file
The workflow can be accessed at usegalaxy.org
