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: UX trial team
Organizations: The University of Manchester
Teams: IBISBA Workflows, nf-core viralrecon, Testing
Organizations: The University of Manchester
Teams: EJPRD WP13 case-studies workflows
Organizations: EJP-RD
https://orcid.org/0000-0002-0637-9950
Our research group "Methods and Algorithms for Bioinformatics" belongs to French National Center for Scientific Research (CNRS) and is hosted by the Computer Science Dpt of University of Montpellier (in the LIRMM joint unit UMR 5506).We offer interactive web services, software, and programming libraries for bioinformatics on the ATGC bioinformatic platform. Well known software from our group are for instance LoRDEC and PhyML.We also support life science projects involving sequencing data analysis ...
Space: Independent Teams
Public web page: http://www.atgc-montpellier.fr/
The Instituto Astrofísica Andalucía (IAA) is an institute belonging to the Consejo Superior de Investigaciones Científicas (CSIC) in Granada - Andalucía. The activities of the IAA - CSIC are related to research in the field of astrophysics and the development of instrumentation for telescopes and spacecraft.
Space: Independent Teams
Public web page: https://www.iaa.csic.es/en
EJPRD WP13 case-studies workflows from phase 1.
Space: Independent Teams
Public web page: https://www.ejprarediseases.org/
SeBiMER is the Bioinformatics Core Facility of IFREMER, the French National Institute for Ocean Science. SeBiMER is in charge of providing a large community of marine biologists with all the requirements (knowledge, softwares and data) to handle small and large scale bioinformatics projects, in a broad range of fields such as metabarcoding (eDNA), (meta-)transcriptomics and genomes assembly & annotaton.
Space: Independent Teams
Public web page: https://ifremer-bioinformatics.github.io/
Genomics Coordination Center, Department of Genetics, University Medical Center Groningen (UMCG)
Space: Independent Teams
Public web page: https://www.rug.nl/research/genetics/genomicscoordinationcentre/
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
Creator: johan Rollin
Submitter: johan Rollin
ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.
Type: Nextflow
Creators: Cyril Noel, Alexandre Cormier, Patrick Durand, Laura Leroi, Pierre Cuzin
Submitter: Patrick Durand
Variant Interpretation Pipeline (VIP) that annotates, filters and reports prioritized causal variants in humans, see https://github.com/molgenis/vip for more information.
Metagenomic dataset taxonomic classification using kraken2
Metagenomic dataset taxonomic classification using kraken2
Workflow for Spliced RNAseq data Steps:
- workflow_quality.cwl:
- FastQC (Read Quality Control)
- fastp (Read Trimming)
- STAR (Read mapping)
- featurecounts (transcript read counts)
- kallisto (transcript [pseudo]counts)
