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- People (149)
- Teams (94)
- Organizations (94)
- Data files (1)
- Publications (3)
- Presentations (2)
- Documents (4+4)
- Workflows (127+12)
Teams: CO2MICS Lab
Organizations: Biomedical Research Foundation (BRFAA) of the Academy of Athens
Teams: UX trial team
Organizations: The University of Manchester
Teams: SKM3
Organizations: The Open University
DARE-FX is assembling leading technology providers from ELIXIR-UK and HDR UK, with three TRE providers and two leading analysis platforms to show through a real reference implementation how we can use secure Research Objects to move between TREs while still supporting the Five Safes principles that govern and protect patient data; all overseen by patient representatives.
Space: Independent Teams
Public web page: https://darefx.uk/
Organisms: Not specified
Space: Independent Teams
Public web page: https://biomedical-big-data.de/
Organisms: Not specified
Computational Science at Helmholtz-Zentrum Dresden-Rossendorf (HZDR)
Space: Independent Teams
Public web page: Not specified
Organisms: Not specified
German Engineering Materials Science Center (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Hereon
Space: Independent Teams
Public web page: https://www.hereon.de/neutrons
Organisms: Not specified
TRON (Translationale Onkologie an der Universitätsmedizin der Johannes Gutenberg-Universität Mainz gemeinnützige GmbH) is an independent biopharmaceutical non-profit translational research organization pursuing new diagnostics and drugs for the treatment of cancer and other diseases with high medical need. We focus our transdisciplinary competencies in genomics and immunology to 1) develop novel platforms for the identification and validation of “omics”-based biomarkers and 2) for harnessing and ...
Space: Independent Teams
Public web page: https://github.com/TRON-Bioinformatics
Organisms: 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
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Publication Type: Unpublished
Citation: arXiv 2105.07028 [cs.DC]
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
DOI: 10.12688/f1000research.54159.1
Citation: F1000Res 10:897
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
DOI: 10.1162/dint_a_00033
Citation: Data Intellegence 2(1-2):108-121
Protein domains can be viewed as building blocks, essential for understanding structure-function relationships in proteins. However, each domain database classifies protein domains using its own methodology. Thus, in many cases, boundaries between different domains or families differ from one domain database to the other, raising the question of domain definition and enumeration. The answer to this question cannot be found in a single database. Rather, expert integration and curation of various ...
Creators: Hrishikesh Dhondge, Isaure Chauvot de Beauchêne, Marie-Dominique Devignes
Submitter: Hrishikesh Dhondge
Creator: Jean-Marie Burel
Submitter: Jean-Marie Burel
Creator: panou@fleming.gr Panou
Submitter: panou@fleming.gr Panou
Creator: johan Rollin
Submitter: johan Rollin
- Deprecated -
See our updated hybrid assembly workflow: https://workflowhub.eu/workflows/367
And other workflows: https://workflowhub.eu/projects/16#workflows
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 ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Jasper Koehorst
Workflow for Illumina Quality Control and Filtering
Multiple paired datasets will be merged into single paired dataset.
Summary:
- FastQC on raw data files
- fastp for read quality trimming
- BBduk for phiX and (optional) rRNA filtering
- Kraken2 for taxonomic classification of reads (optional)
- BBmap for (contamination) filtering using given references (optional)
- FastQC on filtered (merged) data
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default ...
Workflow for LongRead Quality Control and Filtering
- FastQC before filtering (read quality control)
- Filtlong (read trimming)
- Kraken2 taxonomic read classification
- Minimap2 read filtering based on given references
- FastQC after filtering (read quality control)
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here: Tools: https://gitlab.com/m-unlock/cwl Workflows: ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Bart Nijsse
Workflow (hybrid) metagenomic assembly and binning + GEMs
Accepts both Illumina and Nanopore
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Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
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Workflow LongRead Quality: https://workflowhub.eu/workflows/337
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Kraken2 taxonomic classification of FASTQ reads
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SPAdes/Flye (Assembly)
-
QUAST (Assembly quality report)
Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)
- Metabat2/MaxBin2/SemiBin
- DAS Tool
- CheckM
- BUSCO
- GTDB-Tk ...
1. About TF-Prioritizer
This pipeline gives you a full analysis of nfcore chromatine accessibility peak data (ChIP-Seq, ATAC-Seq or DNAse-Seq) and nfcore RNA-seq count data. It performs DESeq2, TEPIC and DYNAMITE including all preprocessing and postprocessing steps necessary to transform the data. It also gives you plots for deep analysis of the data. The general workflow is sketched in the images below:
Graphical abstract:
...